3GVC | pdb_00003gvc

Crystal structure of probable short-chain dehydrogenase-reductase from Mycobacterium tuberculosis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IY8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	Emerald Wizard Full screen condition F6, 20% PEG 3000, 0.1 M Tris, 0.2 M CaCl2, 11.8 mg/mL protein, crystal ID 202293f6, 25% glycerol as cryo-protectant, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.69	α = 90
b = 51.38	β = 94.5
c = 118.84	γ = 90

Symmetry
Space Group	P 1 2 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				2009-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97933	APS	23-ID-D

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	2.45	20	98.8	0.135	7.97			36246		-3	32.734

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	2.45	2.51	99.5		0.561	2.2		2654

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	1IY8	2.45	19.9	36246	1808	98.78	0.195	0.192	0.2	0.247	0.2	RANDOM	25.165

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]
2.84		2.01	-1.98		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.777
r_dihedral_angle_3_deg	15.139
r_dihedral_angle_4_deg	13.464
r_dihedral_angle_1_deg	5.804
r_scangle_it	2.213
r_scbond_it	1.304
r_angle_refined_deg	1.176
r_mcangle_it	0.885
r_angle_other_deg	0.872
r_mcbond_it	0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.777
r_dihedral_angle_3_deg	15.139
r_dihedral_angle_4_deg	13.464
r_dihedral_angle_1_deg	5.804
r_scangle_it	2.213
r_scbond_it	1.304
r_angle_refined_deg	1.176
r_mcangle_it	0.885
r_angle_other_deg	0.872
r_mcbond_it	0.47
r_mcbond_other	0.072
r_chiral_restr	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6983
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.