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The crystal structure of YfnB from Bacillus subtilis subsp. subtilis str. 168
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 3.5M Sodium Format
0.1M Sodium Acetate Trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.93 58.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.186 α = 90 b = 91.186 β = 90 c = 68.253 γ = 120
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 SBC-3 Mirror 2008-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97948 APS 19-BM
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 1.72 26 99.6 0.089 32.2 7.1 34185 34185
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 1.72 1.74 99.9 0.74 1.82 6.9 1337
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.72 25.82 32418 32418 1729 99.62 0.17245 0.17245 0.17113 0.1758 0.19725 0.1977 RANDOM 36.618
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] -0.05 -0.02 -0.05 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.781 r_dihedral_angle_4_deg 19.767 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_1_deg 5.578 r_scangle_it 4.062 r_scbond_it 2.496 r_mcangle_it 1.47 r_angle_refined_deg 1.394 r_mcbond_it 0.846 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.781 r_dihedral_angle_4_deg 19.767 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_1_deg 5.578 r_scangle_it 4.062 r_scbond_it 2.496 r_mcangle_it 1.47 r_angle_refined_deg 1.394 r_mcbond_it 0.846 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1912 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 30
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing DM model building RESOLVE model building HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing