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The crystal structure of SdrE from staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2mol/L CaCl2, 35% PEG 3350, 0.1mol/L, Bis-Tris pH 6.6
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.26 α = 95.59 b = 41.56 β = 97.55 c = 51.14 γ = 99.55
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD MARRESEARCH 2013-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9782 SSRF BL17U
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 1.25 50.32 87 0.056 0.056 8.1 3.7 75580
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 5CF3 1.25 50.32 73166 2416 87.01 0.1444 0.1433 0.1528 0.1764 0.1844 RANDOM 17.096
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] 0.32 0.13 0.34 -0.55 -0.36 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.395 r_sphericity_free 21.636 r_dihedral_angle_4_deg 20.121 r_dihedral_angle_3_deg 13.707 r_sphericity_bonded 12.226 r_rigid_bond_restr 6.908 r_dihedral_angle_1_deg 6.494 r_mcangle_it 2.651 r_angle_refined_deg 2.263 r_mcbond_it 2.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.395 r_sphericity_free 21.636 r_dihedral_angle_4_deg 20.121 r_dihedral_angle_3_deg 13.707 r_sphericity_bonded 12.226 r_rigid_bond_restr 6.908 r_dihedral_angle_1_deg 6.494 r_mcangle_it 2.651 r_angle_refined_deg 2.263 r_mcbond_it 2.221 r_mcbond_other 2.202 r_angle_other_deg 0.957 r_chiral_restr 0.144 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2476 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing