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Staphylococcus aureus lipase - native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 2.0M Sodium Formate, 0.1M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 6.2 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.913 α = 90 b = 129.913 β = 90 c = 251.224 γ = 90
Symmetry Space Group P 41 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 2019-07-19 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 2.08 50 99.9 0.089 0.999 11.6 7.2 246153 47.1
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 2.08 2.21 99.3 2.566 0.481 7.1
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 2hih 2.08 47.74 128855 6444 99.88 0.232 0.231 0.2293 0.2502 0.2495 RANDOM 47.4009
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] 0.84 0.84 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_4_deg 21.158 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_1_deg 7.036 r_mcangle_it 4.45 r_angle_other_deg 4.054 r_mcbond_it 3.481 r_mcbond_other 3.447 r_angle_refined_deg 2.896 r_chiral_restr 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_4_deg 21.158 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_1_deg 7.036 r_mcangle_it 4.45 r_angle_other_deg 4.054 r_mcbond_it 3.481 r_mcbond_other 3.447 r_angle_refined_deg 2.896 r_chiral_restr 0.323 r_bond_refined_d 0.029 r_gen_planes_other 0.018 r_gen_planes_refined 0.012 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6048 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing