2Q3D | pdb_00002q3d

2.2 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylase (OASS) From MYCOBACTERIUM TUBERCULOSIS in Complex with the Reaction Intermediate ALPHA-AMINOACRYLATE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q3B	PDB entry 2Q3B, Holoenzyme

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	293	0.1 M HEPES, 80% MPD. SOAKED WITH 1 mM O-ACETYL-SERINE FOR 30 MINUTES BEFORE FREEZING., pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.785	α = 90
b = 71.785	β = 90
c = 181.179	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MAR CCD 165 mm	First mirror: Water-cooled vertically collimating cylindrical mirror (R = 7300 m). Second mirror: Toroid mirror for horizontal and vertical focusing (R=3300m, R=27mm).	2006-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.000	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	71.8	98.9	0.091	14.2	5.4	24607	24607			43

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	99.8		0.499	2.4	5.3	3550

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2Q3B, Holoenzyme	2.2	28.35	23287	23287	1245	98.49	0.19641	0.19641	0.19379	0.21	0.24943	0.26	RANDOM	30.42

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
3.56			3.56		-7.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.28
r_dihedral_angle_3_deg	16.682
r_dihedral_angle_4_deg	14.801
r_dihedral_angle_1_deg	5.487
r_scangle_it	2.668
r_scbond_it	1.739
r_angle_refined_deg	1.419
r_mcangle_it	0.97
r_mcbond_it	0.581
r_xyhbond_nbd_refined	0.508

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.28
r_dihedral_angle_3_deg	16.682
r_dihedral_angle_4_deg	14.801
r_dihedral_angle_1_deg	5.487
r_scangle_it	2.668
r_scbond_it	1.739
r_angle_refined_deg	1.419
r_mcangle_it	0.97
r_mcbond_it	0.581
r_xyhbond_nbd_refined	0.508
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.233
r_symmetry_hbond_refined	0.221
r_nbd_refined	0.211
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2271
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
MARCCD-mxCube	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.