2P2G | pdb_00002p2g

Crystal Structure of Ornithine Carbamoyltransferase from Mycobacterium Tuberculosis (Rv1656): Orthorhombic Form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FB5	PDB ID 1FB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	273	0.1M Magnesium sulfate, 0.1M HEPES pH 7.5, 10% PEG 8000, 3% ETHANOL, Protein concentration 40mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.166	α = 90
b = 144.646	β = 90
c = 187.769	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315	Vertical focusing mirror	2006-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979462	SSRL	BL9-1

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	2.7	40	97.3	0.163	7.9	3.9	58329	58329			62.4

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	2.7	2.8	90.8		0.675	1.9	3.7	5375

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 ID 1FB5	2.7	38.18	55313	55313	2948	96.67	0.20468	0.20468	0.20172	0.2	0.25903	0.25	RANDOM	43.695

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]
-1.33			0.14		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.464
r_dihedral_angle_3_deg	18.898
r_dihedral_angle_4_deg	18.37
r_dihedral_angle_1_deg	5.918
r_scangle_it	2.314
r_angle_refined_deg	1.401
r_scbond_it	1.373
r_mcangle_it	0.939
r_mcbond_it	0.529
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.464
r_dihedral_angle_3_deg	18.898
r_dihedral_angle_4_deg	18.37
r_dihedral_angle_1_deg	5.918
r_scangle_it	2.314
r_angle_refined_deg	1.401
r_scbond_it	1.373
r_mcangle_it	0.939
r_mcbond_it	0.529
r_nbtor_refined	0.308
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.18
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13487
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	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.