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Crystal structure of human muscle L-lactate dehydrogenase, ternary complex with NADH and oxalate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 18% w/v PEG3350, 50 mM HEPES, pH 6.8, Silver Bullets Bio Screen 1 reagent A1 (Hampton Research), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.55 α = 90 b = 159.62 β = 90 c = 266.16 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 CCD ADSC QUANTUM 315r 2013-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 34 99.9 0.89 14.3 5.5 163776 163531 2 2 37.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2.1 34 2 163531 155268 8172 99.86 0.20777 0.2058 0.209 0.24504 0.244 RANDOM 37.913
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] 3.64 -3.54 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.825 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 14.859 r_dihedral_angle_1_deg 5.913 r_angle_refined_deg 1.266 r_angle_other_deg 0.74 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.825 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 14.859 r_dihedral_angle_1_deg 5.913 r_angle_refined_deg 1.266 r_angle_other_deg 0.74 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 20536 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 434
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling