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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 7 293 1.2 M DL-malic acid, pH 7.0, 2% 1,2-propanol
Crystal Properties Matthews coefficient Solvent content 2.01 38.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.29 α = 90 b = 105.29 β = 90 c = 90.996 γ = 90
Symmetry Space Group I 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 CCD MARMOSAIC 300 mm CCD 2014-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 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 2.59 50 92.5 0.065 0.065 21.4 4.5 8267 7658
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 2.59 2.63 73.1 0.457 3.16 3.8
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 2.59 41.85 7304 354 92.63 0.23092 0.22739 0.2339 0.29768 0.297 RANDOM 90.347
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] 4.2 4.2 -8.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_3_deg 19.522 r_long_range_B_refined 19.206 r_long_range_B_other 19.201 r_scangle_other 14.799 r_dihedral_angle_4_deg 13.345 r_mcangle_it 12.446 r_mcangle_other 12.444 r_dihedral_angle_1_deg 10.466 r_scbond_it 10.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_3_deg 19.522 r_long_range_B_refined 19.206 r_long_range_B_other 19.201 r_scangle_other 14.799 r_dihedral_angle_4_deg 13.345 r_mcangle_it 12.446 r_mcangle_other 12.444 r_dihedral_angle_1_deg 10.466 r_scbond_it 10.192 r_scbond_other 10.187 r_mcbond_it 8.874 r_mcbond_other 8.871 r_angle_refined_deg 1.707 r_angle_other_deg 0.834 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 1832 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing