8P5F | pdb_00008p5f

Human wild-type GAPDH,orthorhombic form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WNC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION		293	20% (w/v) PEG6000, 0.1 M sodium acetate, 0.01 M ZnCl2

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.822	α = 90
b = 132.812	β = 90
c = 146.833	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 4M		2021-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.82	50	100	0.99	14.6	13.3		141893

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85			0.79

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.82	14.995	141552	6994	99.772	0.161	0.1597	0.17	0.1886	0.2	40.885

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]
0.012			-0.004		-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.098
r_dihedral_angle_4_deg	22.203
r_dihedral_angle_3_deg	13.975
r_lrange_it	7.928
r_lrange_other	7.906
r_dihedral_angle_1_deg	7.041
r_scangle_it	6.758
r_scangle_other	6.758
r_scbond_it	4.658
r_scbond_other	4.658
r_mcangle_it	4.568
r_mcangle_other	4.568
r_mcbond_it	3.62
r_mcbond_other	3.61
r_angle_refined_deg	1.726
r_angle_other_deg	1.487
r_nbd_other	0.211
r_nbd_refined	0.204
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.168
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10105
Nucleic Acid Atoms
Solvent Atoms	755
Heterogen Atoms	182

Software

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