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Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 24% PEG4000, 0.2 M lithium sulfate, pH 5.8
Crystal Properties Matthews coefficient Solvent content 3.01 59.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.985 α = 90 b = 101.985 β = 90 c = 127.063 γ = 120
Symmetry Space Group P 32 2 1
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 300 mm CCD 2012-10-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9825 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 50 87.6 0.054 0.054 31.27 5.6 31615 28761
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 2.4 2.44 33.6 0.419 2.67 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.4 47.37 27301 1458 91.02 0.20206 0.19893 0.26222 0.2701 RANDOM 72.462
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] 1.1 1.1 1.1 -3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.24 r_long_range_B_other 20.682 r_long_range_B_refined 20.643 r_dihedral_angle_4_deg 20.563 r_scangle_other 18.544 r_dihedral_angle_3_deg 18.511 r_scbond_it 14.996 r_scbond_other 14.992 r_mcangle_other 13.07 r_mcangle_it 13.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.24 r_long_range_B_other 20.682 r_long_range_B_refined 20.643 r_dihedral_angle_4_deg 20.563 r_scangle_other 18.544 r_dihedral_angle_3_deg 18.511 r_scbond_it 14.996 r_scbond_other 14.992 r_mcangle_other 13.07 r_mcangle_it 13.063 r_mcbond_it 10.533 r_mcbond_other 10.501 r_dihedral_angle_1_deg 7.141 r_angle_refined_deg 1.819 r_angle_other_deg 0.839 r_chiral_restr 0.106 r_bond_refined_d 0.016 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3892 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing