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Rok Repressor Lmo0178 from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F7R PDB entry 5F7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 10 mg/mL proten in 10 mM Tris, pH 8.3, 100 mM sodium chloride against JCSG+ (Qiagen) A10 (0.2 M potassium formate, 20% PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.97 α = 90 b = 81.785 β = 90 c = 141.089 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 225 mm CCD 2015-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.838 70.757 97.7 0.033 27.1 4.8 19017
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 2.838 2.9 98.7 0.628 2.3 5
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 5F7R 2.84 70.757 18018 955 97.13 0.22622 0.22254 0.2236 0.29257 0.289 RANDOM 103.604
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] 1.32 -5.85 4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_3_deg 14.433 r_dihedral_angle_4_deg 14.03 r_long_range_B_refined 13.693 r_long_range_B_other 13.692 r_scangle_other 9.78 r_mcangle_it 9.209 r_mcangle_other 9.208 r_scbond_it 6.337 r_scbond_other 6.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_3_deg 14.433 r_dihedral_angle_4_deg 14.03 r_long_range_B_refined 13.693 r_long_range_B_other 13.692 r_scangle_other 9.78 r_mcangle_it 9.209 r_mcangle_other 9.208 r_scbond_it 6.337 r_scbond_other 6.335 r_mcbond_it 6.063 r_mcbond_other 6.063 r_dihedral_angle_1_deg 3.806 r_angle_refined_deg 1.694 r_angle_other_deg 0.924 r_chiral_restr 0.106 r_gen_planes_refined 0.025 r_gen_planes_other 0.019 r_bond_refined_d 0.013 r_bond_other_d 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 5117 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing