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Reduced form of the transcriptional regulator YodB from B. subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2M sodium bromide and 20%(w/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.78 α = 90 b = 50.798 β = 95.49 c = 50.354 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 ADSC QUANTUM 270 2015-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.0000 PAL/PLS 7A (6B, 6C1)
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 1.7 50.12 99 0.056 44.5 6.2 22351
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 1.7 1.73 0.451
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 4HQM 1.7 50.12 21301 1035 98.72 0.19818 0.19702 0.2075 0.22077 0.221 RANDOM 30.782
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] -0.61 -1 1.07 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.229 r_dihedral_angle_3_deg 13.365 r_dihedral_angle_4_deg 12.673 r_long_range_B_refined 7.4 r_long_range_B_other 7.156 r_dihedral_angle_1_deg 5.076 r_scangle_other 4.61 r_mcangle_it 3.438 r_mcangle_other 3.437 r_scbond_it 2.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.229 r_dihedral_angle_3_deg 13.365 r_dihedral_angle_4_deg 12.673 r_long_range_B_refined 7.4 r_long_range_B_other 7.156 r_dihedral_angle_1_deg 5.076 r_scangle_other 4.61 r_mcangle_it 3.438 r_mcangle_other 3.437 r_scbond_it 2.935 r_scbond_other 2.933 r_mcbond_it 2.239 r_mcbond_other 2.235 r_angle_refined_deg 1.539 r_angle_other_deg 0.945 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 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 1610 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing