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Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 1.8 M ammonium sulfate, 1 mM zinc acetate, 0.1 M citric acid buffer pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.896 α = 90 b = 108.598 β = 90 c = 118.474 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2015-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.1 100 99.7 0.114 0.038 12.4 9.3 37727 33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 99.9 0.608 0.225 2.7 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5Y6U 2.1 80.05 35062 1950 99.49 0.19753 0.1944 0.2036 0.25321 0.2609 RANDOM 39.042
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] -1.19 0.02 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.672 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 10.649 r_long_range_B_refined 8.148 r_long_range_B_other 8.148 r_dihedral_angle_1_deg 6.805 r_scangle_other 5.146 r_mcangle_other 4.28 r_mcangle_it 4.278 r_scbond_it 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.672 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 10.649 r_long_range_B_refined 8.148 r_long_range_B_other 8.148 r_dihedral_angle_1_deg 6.805 r_scangle_other 5.146 r_mcangle_other 4.28 r_mcangle_it 4.278 r_scbond_it 3.256 r_scbond_other 3.254 r_mcbond_it 2.752 r_mcbond_other 2.74 r_angle_refined_deg 1.578 r_angle_other_deg 0.96 r_chiral_restr 0.091 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 4443 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing