7CVP | pdb_00007cvp

The Crystal Structure of human PHGDH from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CWA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M Bis-Tris pH6.5, 25% PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.101	α = 90
b = 121.638	β = 99.974
c = 59.372	γ = 90

Symmetry
Space Group	P 1 21 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		2020-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-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	2.5	42.486	93.7	0.064	6.4	2.3		19518

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	2.5	2.6	94.5		0.13	2.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6CWA	2.5	42.486	19516	944	93.584	0.263	0.2607	0.27	0.3196	0.32	33.884

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]
-4.55		-1.675	10.676		-5.215

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.217
r_dihedral_angle_3_deg	16.568
r_dihedral_angle_4_deg	14
r_dihedral_angle_1_deg	6.941
r_lrange_it	3.979
r_lrange_other	3.978
r_mcangle_it	2.353
r_mcangle_other	2.353
r_scangle_it	1.778
r_scangle_other	1.777
r_mcbond_it	1.403
r_mcbond_other	1.403
r_angle_refined_deg	1.326
r_angle_other_deg	1.114
r_scbond_it	1.066
r_scbond_other	1.066
r_symmetry_xyhbond_nbd_refined	0.194
r_nbd_refined	0.188
r_symmetry_nbd_other	0.178
r_xyhbond_nbd_refined	0.17
r_nbd_other	0.163
r_nbtor_refined	0.143
r_symmetry_nbd_refined	0.141
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.045
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3567
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing