☰ Navigation Tabs
Staphylococcus aureus lipase-Penfluridol complex (in space)
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 COUNTER-DIFFUSION 6.5 293 2.8M Sodum Formate
Crystal Properties Matthews coefficient Solvent content 5.56 78.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.304 α = 90 b = 127.304 β = 90 c = 255.405 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 2023-07-22 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) R Merge I (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 2.57 50 99.8 0.064 0.079 0.996 6.6 7.1 126877
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.72 0.661 0.113 0.396
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.57 47.41 63797 3358 99.16 0.19981 0.19841 0.1978 0.22652 0.2262 RANDOM 91
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] 3.08 3.08 -6.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.929 r_long_range_B_refined 16.873 r_mcangle_it 11.571 r_scbond_it 10.936 r_mcbond_it 8.48 r_dihedral_angle_2_deg 7.81 r_dihedral_angle_1_deg 6.921 r_angle_refined_deg 1.63 r_chiral_restr 0.129 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.929 r_long_range_B_refined 16.873 r_mcangle_it 11.571 r_scbond_it 10.936 r_mcbond_it 8.48 r_dihedral_angle_2_deg 7.81 r_dihedral_angle_1_deg 6.921 r_angle_refined_deg 1.63 r_chiral_restr 0.129 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6048 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing