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Crystal structure of ywiB protein from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 289 lithium chloride, Bis-tris buffer, glycerol, isopropanol, PEG 3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.75 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.428 α = 90 b = 48.428 β = 90 c = 136.156 γ = 120
Symmetry Space Group P 31 2 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 SBC-2 2003-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.03320, 0.97935, 0.97945, 0.96422 APS 19-ID
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 95.2 0.077 6.1 11.6 21269 20248
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 1.76 67 0.396
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD 1.75 45.17 26091 18507 1580 95.11 0.1855 0.1846 0.1957 0.2118 0.1988 random 16.613
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] 0.36 0.18 0.36 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.838 r_scangle_it 3.659 r_scbond_it 2.163 r_mcangle_it 1.513 r_angle_refined_deg 1.363 r_mcbond_it 0.808 r_angle_other_deg 0.752 r_symmetry_vdw_other 0.28 r_nbd_other 0.259 r_symmetry_vdw_refined 0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.838 r_scangle_it 3.659 r_scbond_it 2.163 r_mcangle_it 1.513 r_angle_refined_deg 1.363 r_mcbond_it 0.808 r_angle_other_deg 0.752 r_symmetry_vdw_other 0.28 r_nbd_other 0.259 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.187 r_chiral_restr 0.09 r_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1126 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing SOLVE phasing