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1.7 Angstrom Resolution Crystal Structure of Putative Phosphatase from Clostridium difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 7.1mG/mL, 0.5M Sodium chloride, 0.01M Tris, pH 8.3, Screen: JCSG+, D12, 0.04M Potassium Phosphate, 16% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.333 α = 90 b = 116.333 β = 90 c = 36.08 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD Beryllium lenses 2011-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.7 30 99.2 0.048 35 7.2 26648 26648 -3 29.7
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 1.7 1.73 91.1 0.541 2.8 5.3 1216
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 3MC1 1.7 29.65 25299 25299 1344 99.11 0.16877 0.16877 0.16745 0.186 0.19298 0.2157 RANDOM 39.35
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] -0.78 -0.78 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.621 r_dihedral_angle_3_deg 10.392 r_dihedral_angle_4_deg 5.366 r_scangle_it 4.994 r_scbond_it 3.083 r_dihedral_angle_1_deg 3.044 r_mcangle_it 2.049 r_angle_refined_deg 1.298 r_mcbond_it 1.226 r_angle_other_deg 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.621 r_dihedral_angle_3_deg 10.392 r_dihedral_angle_4_deg 5.366 r_scangle_it 4.994 r_scbond_it 3.083 r_dihedral_angle_1_deg 3.044 r_mcangle_it 2.049 r_angle_refined_deg 1.298 r_mcbond_it 1.226 r_angle_other_deg 0.827 r_mcbond_other 0.381 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1759 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 24
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling