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Crystal structure of human LDHB in complex with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 3350, ammonium acetate, HEPES
Crystal Properties Matthews coefficient Solvent content 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.477 α = 90 b = 84.173 β = 120.76 c = 156.21 γ = 90
Symmetry Space Group C 1 2 1
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 6M 2020-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.8 50 99.6 0.065 0.042 0.994 19.8 3.4 237609
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 100 0.511 0.324 0.736 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1I0Z 1.802 49.993 237609 11844 99.487 0.172 0.1702 0.1799 0.2034 0.2119 29.333
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] -0.578 -0.04 0.336 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_4_deg 24.612 r_dihedral_angle_3_deg 14.82 r_dihedral_angle_1_deg 6.61 r_lrange_it 4.369 r_lrange_other 4.367 r_scangle_it 2.222 r_scangle_other 2.222 r_mcangle_it 1.664 r_mcangle_other 1.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_4_deg 24.612 r_dihedral_angle_3_deg 14.82 r_dihedral_angle_1_deg 6.61 r_lrange_it 4.369 r_lrange_other 4.367 r_scangle_it 2.222 r_scangle_other 2.222 r_mcangle_it 1.664 r_mcangle_other 1.664 r_angle_refined_deg 1.548 r_scbond_it 1.414 r_scbond_other 1.414 r_angle_other_deg 1.373 r_mcbond_it 1.015 r_mcbond_other 1.015 r_symmetry_nbd_refined 0.257 r_nbd_refined 0.2 r_nbd_other 0.194 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20488 Nucleic Acid Atoms Solvent Atoms 977 Heterogen Atoms 484
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing