3QI6 | pdb_00003qi6

Crystal Structure of Cystathionine gamma-synthase MetB (Cgs) from Mycobacterium ulcerans Agy99

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NNP	PDB ENTRY 3NNP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	25.5% PEG4000, 15% glycerol, 170 mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.956	α = 90
b = 106.924	β = 113.67
c = 100.307	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944+	Varimax	2010-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT

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	1.91	44.468	98.1	0.103	7.8	5.2		119042

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	1.91	1.98	89.4		0.263		2.8	10871

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 3NNP	1.91	44.468	118776	5969	97.89	0.2019	0.1998	0.21	0.2413	0.25	RANDOM	16.2273

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]
-0.72		-0.77	1.47		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.091
r_dihedral_angle_4_deg	19.551
r_dihedral_angle_3_deg	13.394
r_dihedral_angle_1_deg	6.84
r_scangle_it	4.275
r_scbond_it	3.047
r_angle_other_deg	2.244
r_angle_refined_deg	2.086
r_mcangle_it	1.765
r_mcbond_it	1.213

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.091
r_dihedral_angle_4_deg	19.551
r_dihedral_angle_3_deg	13.394
r_dihedral_angle_1_deg	6.84
r_scangle_it	4.275
r_scbond_it	3.047
r_angle_other_deg	2.244
r_angle_refined_deg	2.086
r_mcangle_it	1.765
r_mcbond_it	1.213
r_mcbond_other	0.246
r_chiral_restr	0.134
r_bond_refined_d	0.028
r_gen_planes_refined	0.011
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10835
Nucleic Acid Atoms
Solvent Atoms	1440
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.