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Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 292 0.2 M Lithium citrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.51 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.489 α = 90 b = 60.192 β = 108.62 c = 79.107 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 Q315r MIRRORS 2009-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 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 1.76 40 94.5 0.078 18.5 2.9 40514 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 1.76 1.79 59.3 0.415 2.2 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 1.76 40 2 40494 38452 2042 94.8 0.174 0.172 0.2077 0.198 0.2291 RANDOM 13.72
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] -1.08 -1.96 3.47 -3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.455 r_dihedral_angle_4_deg 20.907 r_dihedral_angle_3_deg 14.407 r_dihedral_angle_1_deg 5.28 r_scangle_it 4.704 r_scbond_it 2.874 r_mcangle_it 1.638 r_angle_refined_deg 1.553 r_angle_other_deg 0.934 r_mcbond_it 0.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.455 r_dihedral_angle_4_deg 20.907 r_dihedral_angle_3_deg 14.407 r_dihedral_angle_1_deg 5.28 r_scangle_it 4.704 r_scbond_it 2.874 r_mcangle_it 1.638 r_angle_refined_deg 1.553 r_angle_other_deg 0.934 r_mcbond_it 0.914 r_mcbond_other 0.307 r_chiral_restr 0.099 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2085 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 26
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing MLPHARE phasing SHELXCD phasing SHELXE model building CCP4 model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling CCP4 phasing ARP model building