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Structural and biochemical characterization of a new magnesium ion binding site near Tyr94 in the restriction endonuclease PvuII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PVU PDB ENTRY 1PVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.83 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.18 α = 90 b = 105.28 β = 90 c = 46.67 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH 1997-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 3 8 92.3 0.13 1.8 8104
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1PVU 3 8 8104 808 92.3 0.15 0.15 0.1518 0.2576 RANDOM
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 c_dihedral_angle_d 22 c_scangle_it 14.39 c_mcangle_it 11.76 c_scbond_it 9.89 c_mcbond_it 7.47 c_angle_deg 1.3 c_improper_angle_d 0.79 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 14.39 c_mcangle_it 11.76 c_scbond_it 9.89 c_mcbond_it 7.47 c_angle_deg 1.3 c_improper_angle_d 0.79 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2584 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing