1YGY | pdb_00001ygy

Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	sodium potassium tartrate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.513	α = 90
b = 165.513	β = 90
c = 218.144	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 4		2003-12-14	M	MAD
2	1	x-ray		CCD	ADSC QUANTUM 315		2004-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.97937, 0.97961	APS	14-BM-D
2	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	2.3	50	99.7	0.095	24.7	14.3		78223

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	2.3	2.38	99.9		0.404	4.8	9.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.3	48.8	74263	3918	99.78	0.20715	0.20496	0.201	0.24853	0.2434	RANDOM	36.302

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]
2.72	1.36		2.72		-4.08

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.932
r_dihedral_angle_1_deg	7.202
r_scbond_it	6.574
r_mcangle_it	4.826
r_mcbond_it	3.183
r_angle_refined_deg	1.478
r_nbd_refined	0.255
r_symmetry_hbond_refined	0.254
r_symmetry_vdw_refined	0.246
r_xyhbond_nbd_refined	0.187

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.932
r_dihedral_angle_1_deg	7.202
r_scbond_it	6.574
r_mcangle_it	4.826
r_mcbond_it	3.183
r_angle_refined_deg	1.478
r_nbd_refined	0.255
r_symmetry_hbond_refined	0.254
r_symmetry_vdw_refined	0.246
r_xyhbond_nbd_refined	0.187
r_chiral_restr	0.114
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7672
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	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.