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Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046
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, potassium formate, HEPES
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.389 α = 90 b = 137.577 β = 109.264 c = 84.909 γ = 90
Symmetry Space Group P 1 21 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 2019-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 1.55 50 99.2 0.076 0.042 0.989 20.3 4.1 183405
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 1.55 1.58 93.8 0.251 0.149 0.923 4 3.5
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 1.551 43.496 183364 9146 98.923 0.171 0.1697 0.1787 0.1917 0.1973 23.8
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] -0.534 0.232 0.049 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.144 r_dihedral_angle_4_deg 19.508 r_dihedral_angle_3_deg 11.901 r_dihedral_angle_1_deg 6.418 r_lrange_it 3.065 r_lrange_other 3.058 r_angle_other_deg 1.6 r_dihedral_angle_other_2_deg 1.576 r_angle_refined_deg 1.549 r_scangle_it 1.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.144 r_dihedral_angle_4_deg 19.508 r_dihedral_angle_3_deg 11.901 r_dihedral_angle_1_deg 6.418 r_lrange_it 3.065 r_lrange_other 3.058 r_angle_other_deg 1.6 r_dihedral_angle_other_2_deg 1.576 r_angle_refined_deg 1.549 r_scangle_it 1.247 r_scangle_other 1.247 r_scbond_it 0.969 r_scbond_other 0.969 r_mcangle_it 0.806 r_mcangle_other 0.806 r_mcbond_it 0.642 r_mcbond_other 0.64 r_nbd_other 0.263 r_nbd_refined 0.208 r_symmetry_nbd_other 0.186 r_symmetry_nbd_refined 0.177 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.074 r_bond_refined_d 0.011 r_bond_other_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10244 Nucleic Acid Atoms Solvent Atoms 765 Heterogen Atoms 284
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing