☰ Navigation Tabs
Restriction endonuclease HPY188I in complex with product DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 292 0.1 M MES/NaOH pH 6.2 and 30% MPD. CRYSTAL WAS SOAKED IN 0.1 M CaCl2 FOR 18 H., VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.49 50.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.395 α = 90 b = 65.395 β = 90 c = 221.783 γ = 90
Symmetry Space Group P 41 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 100 CCD MARRESEARCH BENT MIRROR 2010-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.281 MPG/DESY, HAMBURG BW6
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 1.95 20 97.5 0.068 0.068 37.775 13.99 35348 35348 25.2
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) 1.95 1.98 95.8 0.406 0.406 6.488 14.78 1348
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3OQG 1.95 20 35323 35323 1723 97.5 0.17013 0.17013 0.16849 0.1732 0.20144 0.2037 RESOLUTION SHELLS 22.527
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] 0.39 0.39 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.888 r_dihedral_angle_3_deg 14.622 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_1_deg 5.795 r_angle_other_deg 3.943 r_scangle_it 2.161 r_scbond_it 1.551 r_angle_refined_deg 1.281 r_mcangle_it 1.182 r_mcbond_it 0.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.888 r_dihedral_angle_3_deg 14.622 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_1_deg 5.795 r_angle_other_deg 3.943 r_scangle_it 2.161 r_scbond_it 1.551 r_angle_refined_deg 1.281 r_mcangle_it 1.182 r_mcbond_it 0.673 r_symmetry_vdw_other 0.249 r_symmetry_vdw_refined 0.246 r_nbd_other 0.232 r_symmetry_metal_ion_refined 0.231 r_symmetry_hbond_refined 0.198 r_nbd_refined 0.195 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.146 r_nbtor_other 0.112 r_chiral_restr 0.097 r_metal_ion_refined 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2844 Nucleic Acid Atoms 365 Solvent Atoms 311 Heterogen Atoms 7
Software Software Software Name Purpose MAR345 data collection ARP/wARP model building REFMAC refinement DENZO data reduction SCALEPACK data scaling