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High Resolution Crystal Structure of the Wild-Type Restriction-Modification Controller Protein C.Esp1396I (Triclinic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G5G pdb entry 3G5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.1 M MMT buffer, 100 mM Sodium Sulphate, 25% PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.76 α = 110.47 b = 34.78 β = 105.6 c = 41.86 γ = 96
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 2M 2012-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 1.38 37.049 83.5 0.049 14.3 3.8 112030 31070
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 1.38 1.41 83.8 0.37 4 3.8 1570
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 3G5G 1.38 25.79 29524 1470 83.53 0.1505 0.1489 0.1503 0.1815 0.1797 RANDOM 15.78
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] 0.02 0.04 0.02 -0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 22.762 r_dihedral_angle_2_deg 20.565 r_dihedral_angle_3_deg 13.517 r_dihedral_angle_1_deg 5.032 r_angle_refined_deg 2.696 r_angle_other_deg 1.106 r_chiral_restr 0.177 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 22.762 r_dihedral_angle_2_deg 20.565 r_dihedral_angle_3_deg 13.517 r_dihedral_angle_1_deg 5.032 r_angle_refined_deg 2.696 r_angle_other_deg 1.106 r_chiral_restr 0.177 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1258 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 45
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction GDA data collection