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The crystal structure of the ywmB protein from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 10% PEG4000, 45% tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.55 65.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.79 α = 90 b = 50.856 β = 96.49 c = 81.259 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 315 mirrors 2004-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9798 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 2.49 81 96.36 0.071 34 4.5 12266 11820 2 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 2.49 2.55 74.46 0.438 2.37 3.8
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.49 80.85 12266 11820 610 96.36 0.24446 0.24242 0.28134 0.2776 RANDOM 34.22
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] -1.03 1.3 -0.84 2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.887 r_dihedral_angle_4_deg 24.326 r_dihedral_angle_3_deg 21.617 r_dihedral_angle_1_deg 7.26 r_scangle_it 2.572 r_scbond_it 1.482 r_angle_refined_deg 1.386 r_mcangle_it 1.223 r_mcbond_it 0.703 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.887 r_dihedral_angle_4_deg 24.326 r_dihedral_angle_3_deg 21.617 r_dihedral_angle_1_deg 7.26 r_scangle_it 2.572 r_scbond_it 1.482 r_angle_refined_deg 1.386 r_mcangle_it 1.223 r_mcbond_it 0.703 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1700 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling