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Staphylococcus aureus lipase - S116A inactive mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 1.0M Ammonium phosphate dibasic, 0.1M Tris pH8.5
Crystal Properties Matthews coefficient Solvent content 5.3 76.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.209 α = 90 b = 164.209 β = 90 c = 233.053 γ = 120
Symmetry Space Group P 61 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 PIXEL DECTRIS EIGER X 16M 2018-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.59 50 99.8 0.083 0.999 16.8 10.6 109044 65
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 2.59 2.75 2.138 0.523
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 6KSI 2.59 48.81 58006 2901 99.8 0.2503 0.2493 0.2464 0.2675 0.2661 RANDOM 65.5405
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] -0.6 -0.3 -0.6 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.799 r_dihedral_angle_4_deg 24.951 r_dihedral_angle_3_deg 22.649 r_dihedral_angle_1_deg 6.474 r_mcangle_it 6.2 r_mcbond_it 4.314 r_mcbond_other 4.312 r_angle_other_deg 3.93 r_angle_refined_deg 2.122 r_chiral_restr 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.799 r_dihedral_angle_4_deg 24.951 r_dihedral_angle_3_deg 22.649 r_dihedral_angle_1_deg 6.474 r_mcangle_it 6.2 r_mcbond_it 4.314 r_mcbond_other 4.312 r_angle_other_deg 3.93 r_angle_refined_deg 2.122 r_chiral_restr 0.175 r_bond_refined_d 0.018 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6046 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing