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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 4.2 293 25% PEG 4000, 0.45 M ammonium acetate, 0.1 M sodium acetate buffer pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.984 α = 90 b = 96.121 β = 90 c = 263.314 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 95 CCD ADSC QUANTUM 270 2015-06-23 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) 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 2.7 150 93.3 0.115 15.5 11.8 62923 42.2
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 2.7 2.8 91.3 0.733 3.1 11.5
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 5Y6U 2.7 39.912 59674 3166 93.04 0.19046 0.18581 0.27701 0.2839 RANDOM 54.087
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] 0.16 -1.09 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.742 r_dihedral_angle_4_deg 21.469 r_dihedral_angle_3_deg 19.382 r_long_range_B_refined 11.046 r_long_range_B_other 11.046 r_scangle_other 8.396 r_mcangle_it 8.246 r_mcangle_other 8.245 r_dihedral_angle_1_deg 8.136 r_scbond_it 5.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.742 r_dihedral_angle_4_deg 21.469 r_dihedral_angle_3_deg 19.382 r_long_range_B_refined 11.046 r_long_range_B_other 11.046 r_scangle_other 8.396 r_mcangle_it 8.246 r_mcangle_other 8.245 r_dihedral_angle_1_deg 8.136 r_scbond_it 5.668 r_scbond_other 5.667 r_mcbond_it 5.513 r_mcbond_other 5.51 r_angle_refined_deg 2.138 r_angle_other_deg 1.156 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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 16838 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing