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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 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.102 α = 90 b = 94.153 β = 90 c = 118.636 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 MARMOSAIC 300 mm CCD 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 94.9 0.058 30.56 7.4 38668 36685
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 2.03 64 0.51 1.74 3.5
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 THROUGHOUT 2 40 35542 1140 94.87 0.20034 0.19864 0.2108 0.25452 0.2453 RANDOM 50.87
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] -1.2 1.13 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.52 r_long_range_B_other 17.66 r_long_range_B_refined 17.613 r_dihedral_angle_3_deg 16.52 r_scangle_other 15.781 r_dihedral_angle_4_deg 15.136 r_scbond_it 13.344 r_scbond_other 13.332 r_mcangle_other 10.76 r_mcangle_it 10.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.52 r_long_range_B_other 17.66 r_long_range_B_refined 17.613 r_dihedral_angle_3_deg 16.52 r_scangle_other 15.781 r_dihedral_angle_4_deg 15.136 r_scbond_it 13.344 r_scbond_other 13.332 r_mcangle_other 10.76 r_mcangle_it 10.743 r_mcbond_it 9.167 r_mcbond_other 9.119 r_dihedral_angle_1_deg 6.744 r_angle_refined_deg 1.725 r_angle_other_deg 1.454 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.009 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 4052 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing