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Crystal structure of a putative lipoprotein (CD630_1653) from Clostridium difficile 630 at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.16M zinc acetate, 20.0% Glycerol, 14.4% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.508 α = 90 b = 120.508 β = 90 c = 120.508 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2013-07-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795,0.9116,0.9792 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 38.108 99.7 0.124 8.4 5.1 29737 29737
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.9 0.011 1.073 1.6 5.2 2150
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 MAD THROUGHOUT 2.2 38.108 29664 1506 99.34 0.1987 0.1965 0.2077 0.2404 0.2498 RANDOM 48.1296
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.336 r_dihedral_angle_3_deg 12.977 r_dihedral_angle_4_deg 12.063 r_dihedral_angle_1_deg 4.957 r_mcangle_it 2.57 r_mcbond_it 1.62 r_mcbond_other 1.596 r_angle_refined_deg 0.968 r_angle_other_deg 0.695 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.336 r_dihedral_angle_3_deg 12.977 r_dihedral_angle_4_deg 12.063 r_dihedral_angle_1_deg 4.957 r_mcangle_it 2.57 r_mcbond_it 1.62 r_mcbond_other 1.596 r_angle_refined_deg 0.968 r_angle_other_deg 0.695 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3691 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 69
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing SCALA data scaling REFMAC refinement MOSFLM data reduction SHELXD phasing