5NZO

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 1-methyl-3-phenyl-1H-pyrazol-5-amine

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	293	0.1 M PCTP buffer, pH 7 and 23-28 % (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.391	α = 97.05
b = 45.783	β = 110.12
c = 54.807	γ = 106.65

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	0.920	Diamond	I04-1

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	1.29	49.9	82.8	0.091	4	1.94		73976

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.33	84.2		0.917	0.352		1.9	3742

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	1.29	49.88	70307	3651	79.11	0.1984	0.1963	0.2406	RANDOM	20.254

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]
-0.12	0.79	-0.2	-0.2	1.68	-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.383
r_dihedral_angle_2_deg	36.619
r_sphericity_bonded	19.943
r_dihedral_angle_4_deg	16.725
r_dihedral_angle_3_deg	14.362
r_dihedral_angle_1_deg	6.804
r_rigid_bond_restr	4.261
r_angle_refined_deg	1.962
r_angle_other_deg	1.467
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.383
r_dihedral_angle_2_deg	36.619
r_sphericity_bonded	19.943
r_dihedral_angle_4_deg	16.725
r_dihedral_angle_3_deg	14.362
r_dihedral_angle_1_deg	6.804
r_rigid_bond_restr	4.261
r_angle_refined_deg	1.962
r_angle_other_deg	1.467
r_chiral_restr	0.132
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.008
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2920
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	26

Software

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