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The Crystal Structure of human LDHA from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283 0.2M Na malonate, 0.1M Bis-Tris propane pH6.5, 20% PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.959 α = 90 b = 66.479 β = 100.097 c = 250.843 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 2020-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 2.65 46.771 97.9 0.115 7.5 3.2 81570
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 2.65 2.7 0.529
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 4jnk 2.65 46.73 81522 4012 97.468 0.216 0.2125 0.2101 0.2771 0.2744 48.316
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] 1.079 3.034 2.634 -4.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.88 r_dihedral_angle_4_deg 17.514 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_1_deg 6.211 r_lrange_it 4.018 r_lrange_other 4.016 r_mcangle_it 2.394 r_mcangle_other 2.394 r_scangle_it 2.04 r_scangle_other 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.88 r_dihedral_angle_4_deg 17.514 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_1_deg 6.211 r_lrange_it 4.018 r_lrange_other 4.016 r_mcangle_it 2.394 r_mcangle_other 2.394 r_scangle_it 2.04 r_scangle_other 2.04 r_mcbond_it 1.395 r_mcbond_other 1.395 r_angle_refined_deg 1.19 r_scbond_it 1.151 r_scbond_other 1.151 r_angle_other_deg 1.058 r_symmetry_xyhbond_nbd_refined 0.27 r_symmetry_nbd_other 0.17 r_nbd_refined 0.164 r_symmetry_nbd_refined 0.159 r_nbd_other 0.15 r_nbtor_refined 0.142 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.039 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20503 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing