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Crystal structure of putative sporulation-specific glycosylase ydhD from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 100mM Sodium cacodylate pH 7.0, 1.2M Sodium acetate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.72 54.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.965 α = 90 b = 84.965 β = 90 c = 188.041 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 77 CCD MAR CCD 165 mm 2008-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-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 2.15 50 99.9 0.084 5.2 5.6 41723 -0.5 37.4
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 2.15 2.23 99.7 0.74 1.1 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.2 20 37618 1212 99.99 0.19787 0.19597 0.1966 0.25793 0.2534 RANDOM 49.567
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] 0.65 0.32 0.65 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_3_deg 17.194 r_dihedral_angle_4_deg 14.094 r_scangle_it 12.974 r_scbond_it 10.551 r_dihedral_angle_1_deg 9.453 r_mcangle_it 7.339 r_mcbond_it 5.503 r_angle_refined_deg 1.301 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_3_deg 17.194 r_dihedral_angle_4_deg 14.094 r_scangle_it 12.974 r_scbond_it 10.551 r_dihedral_angle_1_deg 9.453 r_mcangle_it 7.339 r_mcbond_it 5.503 r_angle_refined_deg 1.301 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.163 r_nbd_refined 0.133 r_chiral_restr 0.101 r_symmetry_vdw_refined 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 4768 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 48
Software Software Software Name Purpose SHELXD phasing REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling