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The N69Q mutant of Vibrio cholerae endonuclease I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G7E PDB ENTRY 2G7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1 M SODIUM ACETATE, 0.3 M AMMONIUM ACETATE, 10 MM MAGNESIUM SULPHATE, 26% PEG8000, pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.98 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.265 α = 90 b = 64.411 β = 90 c = 75.639 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 RIGAKU R-AXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 25 99.3 0.06 12.8 2.9 22098 20.5
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 1.79 99.1 0.36 2.2 2.8
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 2G7E 1.7 15 20905 1131 99 0.2 0.197 0.2011 0.259 0.2606 RANDOM 12.93
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] -0.25 0.06 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.361 r_dihedral_angle_4_deg 14.381 r_dihedral_angle_3_deg 12.495 r_dihedral_angle_1_deg 6.283 r_scangle_it 3.191 r_scbond_it 2.305 r_angle_refined_deg 1.52 r_mcangle_it 1.333 r_mcbond_it 1.171 r_angle_other_deg 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.361 r_dihedral_angle_4_deg 14.381 r_dihedral_angle_3_deg 12.495 r_dihedral_angle_1_deg 6.283 r_scangle_it 3.191 r_scbond_it 2.305 r_angle_refined_deg 1.52 r_mcangle_it 1.333 r_mcbond_it 1.171 r_angle_other_deg 0.974 r_symmetry_vdw_other 0.286 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.196 r_nbd_other 0.195 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.088 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1672 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing