3H9E | pdb_00003h9e

Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) complex with NAD and phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VYV	2VYV, CHAIN D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277.15	20% PEG 3350; 0.2M Na/K phosphate; 10% Ethylene glycol (protein buffer 10mM Tris, pH 8.5; 0.1M NaCl), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.96	α = 90
b = 71.78	β = 122.9
c = 81.26	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315	Kirkpatrick Baez bimorph mirror pair	2009-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.72	68.23	99.2	0.077	11.4	4.4	72853	72227		2	22.6

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	1.72	1.81	96.3		0.514	2.3	3.6	10230

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2VYV, CHAIN D	1.72	68.23	72225	70229	1996	99.14	0.143	0.1439	0.143	0.15	0.17573	0.18	RANDOM	13.953

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]
0.58		-0.54	-0.14		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.47
r_dihedral_angle_4_deg	15.367
r_dihedral_angle_3_deg	12.25
r_scangle_it	6.993
r_dihedral_angle_1_deg	6.318
r_scbond_it	4.81
r_mcangle_it	3.163
r_mcbond_it	2.032
r_angle_refined_deg	1.497
r_angle_other_deg	0.929

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.47
r_dihedral_angle_4_deg	15.367
r_dihedral_angle_3_deg	12.25
r_scangle_it	6.993
r_dihedral_angle_1_deg	6.318
r_scbond_it	4.81
r_mcangle_it	3.163
r_mcbond_it	2.032
r_angle_refined_deg	1.497
r_angle_other_deg	0.929
r_mcbond_other	0.505
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5146
Nucleic Acid Atoms
Solvent Atoms	467
Heterogen Atoms	164

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.