☰ Navigation Tabs
Crystal structure of GAPDH complexed with arsenate from Lactiplantibacillus plantarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 25%(w/v) PEG 1500, 0.1 M MIB buffer
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.85 α = 90 b = 123.964 β = 90 c = 132.859 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 PILATUS3 S 2M 2022-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.87 48.49 99.8 0.088 0.104 0.056 0.998 13.1 6.5 69658
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 99.9 0.908 0.574 0.762 2.1 6.5
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 (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 2.16 45.59 65890 3572 99.74 0.21835 0.21606 0.2249 0.2614 0.2682 RANDOM 32.668
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] 0.75 -0.51 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.705 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 15.723 r_long_range_B_refined 13.464 r_long_range_B_other 13.37 r_dihedral_angle_1_deg 7.878 r_scangle_other 4.086 r_mcangle_it 3.956 r_mcangle_other 3.955 r_scbond_it 2.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.705 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 15.723 r_long_range_B_refined 13.464 r_long_range_B_other 13.37 r_dihedral_angle_1_deg 7.878 r_scangle_other 4.086 r_mcangle_it 3.956 r_mcangle_other 3.955 r_scbond_it 2.642 r_scbond_other 2.642 r_mcbond_it 2.581 r_mcbond_other 2.581 r_angle_refined_deg 1.496 r_angle_other_deg 1.282 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9950 Nucleic Acid Atoms Solvent Atoms 837 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing