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ROK repressor Lmo0178 from Listeria monocytogenes bound to inducer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 9.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II D6 (Qiagen, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 1.77 30.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.2 α = 90 b = 95.064 β = 90 c = 117.144 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 2015-04-27 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 1.8 30 99.9 0.051 24.1 5.6 55352
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 1.8 1.85 100 0.567 2.7 5.6
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 in-house structure 1.85 30 52630 2664 99.79 0.1682 0.16659 0.1758 0.20029 0.2084 RANDOM 32.369
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] 0.3 -0.06 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.52 r_dihedral_angle_4_deg 19.465 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 6.486 r_long_range_B_refined 5.263 r_long_range_B_other 5.263 r_scangle_other 2.378 r_mcangle_it 1.754 r_mcangle_other 1.754 r_scbond_it 1.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.52 r_dihedral_angle_4_deg 19.465 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 6.486 r_long_range_B_refined 5.263 r_long_range_B_other 5.263 r_scangle_other 2.378 r_mcangle_it 1.754 r_mcangle_other 1.754 r_scbond_it 1.454 r_scbond_other 1.442 r_angle_refined_deg 1.253 r_mcbond_it 1.07 r_mcbond_other 1.069 r_angle_other_deg 0.76 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 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 4731 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing