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Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.75-2.0 M ammonium sulfate, 0.1 M HEPES pH 7.0, and 0-0.5% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.594 α = 90 b = 103.402 β = 90 c = 51.623 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU SATURN 944+ 2010-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.541
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 2.06 50 95 0.095 11.9 5.4 24431
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 2.06 2.13 68.9 0.525 2.1 1726
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 FOURIER SYNTHESIS THROUGHOUT 5c7Q 2.06 26.8 23061 1256 95.08 0.1845 0.1812 0.245 0.2376 RANDOM 31.191
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] 1.3 -0.58 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.768 r_dihedral_angle_4_deg 21.497 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_1_deg 6.627 r_mcangle_it 3.18 r_mcbond_it 2.204 r_mcbond_other 2.202 r_angle_refined_deg 1.886 r_angle_other_deg 0.832 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.768 r_dihedral_angle_4_deg 21.497 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_1_deg 6.627 r_mcangle_it 3.18 r_mcbond_it 2.204 r_mcbond_other 2.202 r_angle_refined_deg 1.886 r_angle_other_deg 0.832 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2975 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 169
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction REFMAC refinement REFMAC phasing