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Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VT3 PDB ENTRY 2VT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.1 20% PEG6000, 0.2M NH4CL, 0.1M HEPES PH 7.1
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.29 α = 90 b = 53.74 β = 125.55 c = 86.89 γ = 90
Symmetry Space Group C 1 2 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 MARRESEARCH 2007-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-5 MAX II I911-5
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 2.3 30 97.9 0.01 19.1 3.7 21294 5
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 2.4 98.5 0.04 5 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VT3 2.3 28.61 20229 1065 100 0.221 0.217 0.28 0.2868 RANDOM 30.22
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] -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.352 r_dihedral_angle_3_deg 17.687 r_dihedral_angle_4_deg 15.784 r_dihedral_angle_1_deg 6.123 r_scangle_it 2.659 r_scbond_it 1.813 r_angle_refined_deg 1.643 r_angle_other_deg 1.643 r_mcangle_it 1.285 r_mcbond_it 0.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.352 r_dihedral_angle_3_deg 17.687 r_dihedral_angle_4_deg 15.784 r_dihedral_angle_1_deg 6.123 r_scangle_it 2.659 r_scbond_it 1.813 r_angle_refined_deg 1.643 r_angle_other_deg 1.643 r_mcangle_it 1.285 r_mcbond_it 0.741 r_nbtor_refined 0.303 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_bond_other_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3060 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling