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ROK repressor Lmo0178 from Listeria monocytogenes bound to operator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 7.5 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II H6 (Qiagen, 0.2 M sodium formate, 20% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.672 α = 90 b = 180.257 β = 89.97 c = 79.86 γ = 90
Symmetry Space Group P 1 21 1
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 2.4 30 100 0.067 28.7 5.5 81757
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 2.4 2.44 100 0.71 5.5
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 5F7R 2.4 30 77556 4010 99.6 0.184 0.182 0.186 0.218 0.2204 RANDOM 58.79
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] 0.1 -0.33 1.13 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 12.913 r_dihedral_angle_3_deg 11.384 r_dihedral_angle_1_deg 6.165 r_long_range_B_refined 6.005 r_long_range_B_other 6.005 r_scangle_other 4.184 r_mcangle_it 3.088 r_mcangle_other 3.088 r_scbond_it 2.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 12.913 r_dihedral_angle_3_deg 11.384 r_dihedral_angle_1_deg 6.165 r_long_range_B_refined 6.005 r_long_range_B_other 6.005 r_scangle_other 4.184 r_mcangle_it 3.088 r_mcangle_other 3.088 r_scbond_it 2.655 r_scbond_other 2.655 r_mcbond_it 1.991 r_mcbond_other 1.991 r_angle_refined_deg 1.453 r_angle_other_deg 0.955 r_chiral_restr 0.089 r_gen_planes_refined 0.023 r_gen_planes_other 0.018 r_bond_refined_d 0.01 r_bond_other_d 0.002 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 12220 Nucleic Acid Atoms 1394 Solvent Atoms 273 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing