5N53

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.1 M PCTP, pH 7, 23-25 % PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.353	α = 97.9
b = 45.323	β = 110.06
c = 55.255	γ = 106.35

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS3 S 6M		2014-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.48	50.12	86.1	0.111	0.1	4.6	2.13		51238

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	85.8		1.088	0.972	0.355	0.9	2.14

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2G76	1.48	50.12	48587	2651	84.57	0.1919	0.1891	0.2435	RANDOM	19.681

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]
-0.04	-0.47	0.68	-0.58	1.25	-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.191
r_sphericity_free	36.748
r_sphericity_bonded	21.853
r_dihedral_angle_4_deg	20.453
r_dihedral_angle_3_deg	17.769
r_dihedral_angle_1_deg	6.947
r_rigid_bond_restr	4.372
r_angle_refined_deg	1.978
r_angle_other_deg	1.412
r_chiral_restr	0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.191
r_sphericity_free	36.748
r_sphericity_bonded	21.853
r_dihedral_angle_4_deg	20.453
r_dihedral_angle_3_deg	17.769
r_dihedral_angle_1_deg	6.947
r_rigid_bond_restr	4.372
r_angle_refined_deg	1.978
r_angle_other_deg	1.412
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2920
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	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.