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The crystal structure of L-leucine dehydrogenase from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 12 % (w/v) polyethylene glycol 3,350, 0.1M sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.62 α = 90 b = 90.18 β = 90 c = 61.22 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 6M 2020-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9794 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.5 90.2 99.8 0.16 0.998 13.4 11.6 28028 47.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 1.42 0.714 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1LEH 2.5 76.22 1.35 27974 1404 99.66 0.1983 0.1956 0.1969 0.2486 0.2481 46.17
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.1564 f_angle_d 0.9684 f_chiral_restr 0.0526 f_plane_restr 0.0079 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4814 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling MrBUMP phasing