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Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E52 PDB ENTRY 2E52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG3350, ammonium acetate, Magnesium ion, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.99 58.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.46 α = 90 b = 132.211 β = 111.03 c = 94.07 γ = 90
Symmetry Space Group P 1 21 1
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 4r mirror 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.000 Photon Factory BL-6A
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 2.17 50 99.8 0.063 24.7 1.9 100664
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 2.17 2.23 98 0.404 3.5
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 2E52 2.17 41.67 100399 5018 99.77 0.18 0.178 0.1767 0.226 0.2248 RANDOM 36.106
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] 0.05 0.53 0.51 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.522 r_dihedral_angle_3_deg 16.57 r_dihedral_angle_4_deg 15.567 r_dihedral_angle_1_deg 6.215 r_scangle_it 4.287 r_scbond_it 2.804 r_mcangle_it 1.829 r_angle_refined_deg 1.779 r_mcbond_it 0.969 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.522 r_dihedral_angle_3_deg 16.57 r_dihedral_angle_4_deg 15.567 r_dihedral_angle_1_deg 6.215 r_scangle_it 4.287 r_scbond_it 2.804 r_mcangle_it 1.829 r_angle_refined_deg 1.779 r_mcbond_it 0.969 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9775 Nucleic Acid Atoms 1462 Solvent Atoms 573 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing