☰ Navigation Tabs
Crystal structure of the serine endoprotease from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 20% PEG 4000, 10% Isopropane, 50 mM CAPSO buffer pH 11, 0.1 M Sodium citrate pH 5.6, 5% P200 paratone-N oil
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.418 α = 90 b = 104.418 β = 90 c = 76.015 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD beryllium lenses 2016-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 30 100 0.1 15.8 7.1 26479
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.65 3.3 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RQY 1.85 30 25187 1292 99.91 0.14999 0.14831 0.18269 0.1984 RANDOM 46.116
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] -0.38 -0.19 -0.38 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.475 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_4_deg 14.846 r_long_range_B_refined 7.968 r_long_range_B_other 7.966 r_dihedral_angle_1_deg 7.236 r_scangle_other 4.613 r_mcangle_it 3.809 r_mcangle_other 3.808 r_scbond_it 2.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.475 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_4_deg 14.846 r_long_range_B_refined 7.968 r_long_range_B_other 7.966 r_dihedral_angle_1_deg 7.236 r_scangle_other 4.613 r_mcangle_it 3.809 r_mcangle_other 3.808 r_scbond_it 2.889 r_scbond_other 2.881 r_mcbond_it 2.333 r_mcbond_other 2.331 r_angle_refined_deg 2.003 r_angle_other_deg 1.048 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2017 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHENIX phasing Coot model building