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MarR Protein from Peptoclostridium difficile DA00132
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 289 8~10% 2-Propanol, 0.1 M Tris-Cl
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.569 α = 90 b = 66.569 β = 90 c = 83.654 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD RIGAKU 2015-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.987 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.297 50 93.8 77 20 8352
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 2.3 2.34 98.8 0.584 16.87 15
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 1LJ9 2.3 25.73 7915 394 93.73 0.21332 0.21151 0.2199 0.25012 0.2433 RANDOM 60.319
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] 0.09 0.09 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.44 r_dihedral_angle_3_deg 20.833 r_long_range_B_refined 13.386 r_long_range_B_other 13.385 r_dihedral_angle_4_deg 13.36 r_scangle_other 11.669 r_scbond_it 7.744 r_scbond_other 7.739 r_mcangle_it 6.702 r_mcangle_other 6.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.44 r_dihedral_angle_3_deg 20.833 r_long_range_B_refined 13.386 r_long_range_B_other 13.385 r_dihedral_angle_4_deg 13.36 r_scangle_other 11.669 r_scbond_it 7.744 r_scbond_other 7.739 r_mcangle_it 6.702 r_mcangle_other 6.698 r_dihedral_angle_1_deg 5.871 r_mcbond_other 5.187 r_mcbond_it 5.184 r_angle_refined_deg 1.789 r_angle_other_deg 0.873 r_chiral_restr 0.098 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 1246 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing Coot model building