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Crystal structure of the quinone-bound YodB from B. subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HS7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2 M sodium citrate tribasic dihydrate and 30% (w/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 1.89 34.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.941 α = 90 b = 51.178 β = 93.46 c = 48.391 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 315r 2015-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0000 PAL/PLS 5C (4A)
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 2.1 30 96 0.07 36.9 3.9 10779
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 2.1 2.14 0.629
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 5HS7 2.1 30 10221 540 95.76 0.24591 0.24438 0.2762 0.2842 RANDOM 65.313
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] 2.19 -1.39 -2.58 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_4_deg 14.634 r_long_range_B_refined 12.726 r_long_range_B_other 12.726 r_scangle_other 10.269 r_scbond_it 6.408 r_scbond_other 6.404 r_dihedral_angle_1_deg 6.297 r_mcangle_it 6.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_4_deg 14.634 r_long_range_B_refined 12.726 r_long_range_B_other 12.726 r_scangle_other 10.269 r_scbond_it 6.408 r_scbond_other 6.404 r_dihedral_angle_1_deg 6.297 r_mcangle_it 6.193 r_mcangle_other 6.19 r_mcbond_it 4.743 r_mcbond_other 4.743 r_angle_refined_deg 1.481 r_angle_other_deg 0.949 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 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 1446 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing