2P9G | pdb_00002p9g

Crystal structure of serine bound G336V,G337V double mutant of E.coli phosphoglycerate dehydrogenase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PSD	pdb entry 1PSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	30% PEG 400, 0.1M acetate, 0.2M Calcium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.072	α = 90
b = 132.239	β = 90
c = 52.37	γ = 90

Symmetry
Space Group	P 21 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		IMAGE PLATE	RIGAKU RAXIS IV	monochromator	2006-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.541

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	2.8	40.32	99.5	0.052	20.1	3.3		25289

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	2.8	2.95	100		0.207	4.8	3.3

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 1PSD	2.8	35	23997	1285	99.2	0.20004	0.19737	0.1908	0.25008	0.2509	RANDOM	44.721

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]
-3.14			-3		6.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.971
r_dihedral_angle_4_deg	23.879
r_dihedral_angle_3_deg	18.899
r_scbond_it	8.101
r_dihedral_angle_1_deg	6.421
r_mcangle_it	6.244
r_mcbond_it	4.074
r_angle_refined_deg	1.869
r_nbtor_refined	0.344
r_nbd_refined	0.274

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.971
r_dihedral_angle_4_deg	23.879
r_dihedral_angle_3_deg	18.899
r_scbond_it	8.101
r_dihedral_angle_1_deg	6.421
r_mcangle_it	6.244
r_mcbond_it	4.074
r_angle_refined_deg	1.869
r_nbtor_refined	0.344
r_nbd_refined	0.274
r_symmetry_hbond_refined	0.261
r_xyhbond_nbd_refined	0.216
r_symmetry_vdw_refined	0.187
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6130
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	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.