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Human wild-type GAPDH,orthorhombic form
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 0.1696 0.1886 0.1966 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
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