9T7U | pdb_00009t7u

Glyceraldehyde-3-phosphate dehydrogenase A (GAPDH)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	200 mM sodium acetate, 100 mM Bis Tris propane, pH 6.5, and 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.901	α = 90
b = 98.901	β = 90
c = 252.217	γ = 90

Symmetry
Space Group	P 43 21 2

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 PILATUS 6M		2016-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.98	Diamond	I02

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	1.7	46.83	100	0.999	14.3	14.1		137953

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	1.7	1.73			0.612		13.9

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	1.7	46.83	137818	6948	99.984	0.155	0.1524	0.1524	0.2094	0.2096	30.742

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]
-1.749			-1.749		3.498

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.992
r_dihedral_angle_4_deg	20.943
r_rigid_bond_restr	13.856
r_dihedral_angle_3_deg	13.092
r_lrange_it	8.156
r_scangle_it	7.498
r_scbond_it	7.245
r_dihedral_angle_1_deg	6.644
r_mcangle_it	5.33
r_mcbond_it	4.6
r_angle_refined_deg	1.777
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.183
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.124
r_metal_ion_refined	0.111
r_ncsr_local_group_2	0.1
r_ncsr_local_group_4	0.091
r_ncsr_local_group_3	0.088
r_ncsr_local_group_5	0.087
r_ncsr_local_group_6	0.087
r_ncsr_local_group_1	0.078
r_bond_refined_d	0.017
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10109
Nucleic Acid Atoms
Solvent Atoms	631
Heterogen Atoms	55

Software

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