☰ Navigation Tabs
Crystal structure of Yersinia pestis YopH in complex with an aminooxy- containing platform compound for inhibitor design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QZ0 PDB ENTRY 1QZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 MOLECULAR DIMENSIONS MORPHEUS SCREEN CONDITION D8 (0.1M BUFFER SYSTEM 2, PH 7.5, 0.12M ALCOHOLS, 12.5% V/V MPD, 12.5% W/V PEG 1000, 12.5% W/V PEG 3350).
Crystal Properties Matthews coefficient Solvent content 2.04 39.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.243 α = 90 b = 55.48 β = 90 c = 100.081 γ = 90
Symmetry Space Group P 21 21 21
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 MARESEARCH MX-300 2010-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1.78 50 92.8 0.11 21.9 5.9 25241 2
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 1.78 1.8 74.8 0.5 2.3 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QZ0 1.78 50 23875 1268 92.39 0.16685 0.16457 0.21007 0.2029 RANDOM 13.168
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] -0.99 -0.9 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_1_deg 5.985 r_scangle_it 4.065 r_scbond_it 2.555 r_mcangle_it 1.54 r_angle_refined_deg 1.487 r_angle_other_deg 0.904 r_mcbond_it 0.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_1_deg 5.985 r_scangle_it 4.065 r_scbond_it 2.555 r_mcangle_it 1.54 r_angle_refined_deg 1.487 r_angle_other_deg 0.904 r_mcbond_it 0.813 r_mcbond_other 0.236 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 2165 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing