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Rabbit Muscle L-lactate dehydrogenase in complex with citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 10 % PEG 3350, 0.1 M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.705 α = 114.55 b = 141.571 β = 94.69 c = 148.136 γ = 102.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2019-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.98 SLS X06DA
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 2.6 49.02 93.44 0.97 5 2.1 162132
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 2.6 2.66 0.557
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 5nqb 2.6 49.02 162132 8434 93.44 0.2016 0.1986 0.205 0.2595 0.2614 RANDOM 33.984
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] 2.1 -0.01 -0.41 0.52 -1.78 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.919 r_dihedral_angle_4_deg 20.955 r_dihedral_angle_3_deg 17.306 r_dihedral_angle_1_deg 7.275 r_angle_refined_deg 1.422 r_angle_other_deg 1.174 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.919 r_dihedral_angle_4_deg 20.955 r_dihedral_angle_3_deg 17.306 r_dihedral_angle_1_deg 7.275 r_angle_refined_deg 1.422 r_angle_other_deg 1.174 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40303 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing