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Crystal structure of lactate dehydrogenase from Selenomonas ruminantium with NADH.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 21 % PEG 1500
150 mM Malonate-Imidazole-Boric Acid pH 5 (MIB-PACT)
10 mM Sodium Bicarbonate pH 8
10 mM Tb-XO4
Crystal Properties Matthews coefficient Solvent content 2.53 51.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.75 α = 90 b = 104.26 β = 90 c = 110.94 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2020-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Xenocs GeniX 3D Cu HF 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.84 38.61 99.9 0.99 12.17 5.6 31954
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.95 99.9 0.83 5.3
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 (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 3D0O 1.84 38.61 28758 3196 99.9 0.149 0.145 0.1584 0.188 0.1961 RANDOM 18.2
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] -1.3 0.9 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.614 r_dihedral_angle_4_deg 14.776 r_dihedral_angle_3_deg 13.16 r_dihedral_angle_1_deg 6.875 r_angle_refined_deg 1.596 r_angle_other_deg 1.451 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.614 r_dihedral_angle_4_deg 14.776 r_dihedral_angle_3_deg 13.16 r_dihedral_angle_1_deg 6.875 r_angle_refined_deg 1.596 r_angle_other_deg 1.451 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2496 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing