8P5F

Human wild-type GAPDH,orthorhombic form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WNC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION29320% (w/v) PEG6000, 0.1 M sodium acetate, 0.01 M ZnCl2
Crystal Properties
Matthews coefficientSolvent content
2.7354.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.822α = 90
b = 132.812β = 90
c = 146.833γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2021-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.9000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.82501000.9914.613.3141893
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.850.79

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.8214.995141552699499.7720.1610.15970.188640.885
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.098
r_dihedral_angle_4_deg22.203
r_dihedral_angle_3_deg13.975
r_lrange_it7.928
r_lrange_other7.906
r_dihedral_angle_1_deg7.041
r_scangle_it6.758
r_scangle_other6.758
r_scbond_it4.658
r_scbond_other4.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.098
r_dihedral_angle_4_deg22.203
r_dihedral_angle_3_deg13.975
r_lrange_it7.928
r_lrange_other7.906
r_dihedral_angle_1_deg7.041
r_scangle_it6.758
r_scangle_other6.758
r_scbond_it4.658
r_scbond_other4.658
r_mcangle_it4.568
r_mcangle_other4.568
r_mcbond_it3.62
r_mcbond_other3.61
r_angle_refined_deg1.726
r_angle_other_deg1.487
r_nbd_other0.211
r_nbd_refined0.204
r_symmetry_nbd_refined0.192
r_symmetry_nbd_other0.183
r_xyhbond_nbd_refined0.178
r_symmetry_xyhbond_nbd_refined0.173
r_nbtor_refined0.168
r_chiral_restr0.088
r_symmetry_nbtor_other0.083
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10105
Nucleic Acid Atoms
Solvent Atoms755
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing