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Structure of a putative oxidoreductase from Rickettsia felis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZ1 PDB ENTRY 1RZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 17 mg/mL RifeA.00250.a, 0.2 M potassium thiocyanate, 20% PEG3350, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.58 α = 90 b = 79.73 β = 90 c = 155.14 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 ADSC QUANTUM 315r 2013-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97856 SSRL BL7-1
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 2 42.941 98 0.095 15.07 44103 -3 28.186
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 2.05 97.6 0.513 3.77
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RZ1 2 19.79 44048 2219 98 0.184 0.1816 0.19 0.229 0.234 RANDOM 25.3303
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] -0.21 1.94 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.956 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_4_deg 11.558 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.418 r_mcangle_it 1.392 r_mcbond_it 0.844 r_mcbond_other 0.842 r_angle_other_deg 0.767 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.956 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_4_deg 11.558 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.418 r_mcangle_it 1.392 r_mcbond_it 0.844 r_mcbond_other 0.842 r_angle_other_deg 0.767 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4869 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 51
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction