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Gossypol bound lactate dehydrogenase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 8% Tacsimate (pH 7.0), 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.369 α = 89.98 b = 110.924 β = 90.04 c = 217.546 γ = 88.37
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2018-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.98 35.56 97.02 0.051 9.3 2.53 63704
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.07 4.17 0.051 9.3
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 3.98 35.56 63704 3390 99.06 0.2401 0.23839 0.2442 0.27315 0.2792 RANDOM 53.977
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] -0.01 0.17 0.06 -0.01 -0.1 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.441 r_dihedral_angle_4_deg 19.188 r_long_range_B_refined 17.797 r_dihedral_angle_3_deg 17.71 r_dihedral_angle_1_deg 6.831 r_mcangle_it 6.597 r_mcbond_it 3.744 r_scbond_it 3.346 r_angle_refined_deg 1.63 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.441 r_dihedral_angle_4_deg 19.188 r_long_range_B_refined 17.797 r_dihedral_angle_3_deg 17.71 r_dihedral_angle_1_deg 6.831 r_mcangle_it 6.597 r_mcbond_it 3.744 r_scbond_it 3.346 r_angle_refined_deg 1.63 r_chiral_restr 0.156 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 61632 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction