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Crystal Structure of the Restriction-Modification Controller Protein C.Csp231I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y7Y PDB Entry 1Y7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.1M Na HEPES, 1.4M Tri-sodium citrate dihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.37 α = 90 b = 137.37 β = 90 c = 137.37 γ = 90
Symmetry Space Group F 41 3 2
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 315 2009-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 50 97.2 0.072 42.78 38.7 7979 7753 35.293
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 2.1 94.2 0.408 11.3 38.8 991
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 (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 PDB Entry 1Y7Y 2 19.24 7931 7566 365 99.92 0.178 0.176 0.1765 0.225 0.2221 RANDOM 41.169
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 41.394 r_dihedral_angle_3_deg 16.978 r_dihedral_angle_4_deg 14.519 r_dihedral_angle_1_deg 5.941 r_scangle_it 5.924 r_scbond_it 3.595 r_mcangle_it 2.29 r_angle_refined_deg 1.753 r_mcbond_it 1.268 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.394 r_dihedral_angle_3_deg 16.978 r_dihedral_angle_4_deg 14.519 r_dihedral_angle_1_deg 5.941 r_scangle_it 5.924 r_scbond_it 3.595 r_mcangle_it 2.29 r_angle_refined_deg 1.753 r_mcbond_it 1.268 r_chiral_restr 0.14 r_bond_refined_d 0.023 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 784 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction GDA data collection XDS data reduction