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Glyceraldehyde-3-phosphate dehydrogenase A (GAPDH)
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
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