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Crystal Structure of an R35A mutant of the Restriction-Modification Controller Protein C.Esp1396I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CLC PDB ENTRY 3CLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 precipitation 8 277 150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.03 39.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.435 α = 90 b = 48.435 β = 90 c = 135.78 γ = 120
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 4 2008-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.952 41.959 100 0.263 0.263 1.394 7.6 3840 3839 86
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 2.95 3.11 100 0.412 0.412 1.9 5.5 553
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CLC 3 35.69 3615 164 100 0.249 0.248 0.2517 0.267 0.2751 RANDOM 56.744
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] 0.42 0.21 0.42 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.249 r_dihedral_angle_3_deg 24.613 r_dihedral_angle_4_deg 23.701 r_dihedral_angle_1_deg 5.971 r_angle_refined_deg 1.69 r_scangle_it 1.264 r_scbond_it 0.803 r_mcangle_it 0.623 r_symmetry_vdw_refined 0.409 r_mcbond_it 0.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.249 r_dihedral_angle_3_deg 24.613 r_dihedral_angle_4_deg 23.701 r_dihedral_angle_1_deg 5.971 r_angle_refined_deg 1.69 r_scangle_it 1.264 r_scbond_it 0.803 r_mcangle_it 0.623 r_symmetry_vdw_refined 0.409 r_mcbond_it 0.401 r_symmetry_hbond_refined 0.35 r_nbtor_refined 0.326 r_nbd_refined 0.261 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.126 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1208 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection