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Restriction endonuclease HPY188I in complex with substrate DNA
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, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.236 α = 90 b = 65.236 β = 90 c = 220.63 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 2010-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 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 1.75 20 98 0.061 0.061 24.651 5.55 48330 48330 23.2
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) 1.75 1.77 97.1 0.44 0.44 3.265 5.55 1895
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.75 19.9 48287 48287 2393 98 0.16612 0.16612 0.16474 0.1682 0.19218 0.1936 RESOLUTION SHELLS 20.972
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] 0.7 0.7 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.222 r_dihedral_angle_3_deg 15.094 r_dihedral_angle_4_deg 13.779 r_dihedral_angle_1_deg 5.58 r_angle_other_deg 3.961 r_scangle_it 2.251 r_scbond_it 1.492 r_angle_refined_deg 1.224 r_mcangle_it 1.107 r_mcbond_it 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.222 r_dihedral_angle_3_deg 15.094 r_dihedral_angle_4_deg 13.779 r_dihedral_angle_1_deg 5.58 r_angle_other_deg 3.961 r_scangle_it 2.251 r_scbond_it 1.492 r_angle_refined_deg 1.224 r_mcangle_it 1.107 r_mcbond_it 0.6 r_nbd_other 0.23 r_symmetry_vdw_other 0.23 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.208 r_nbtor_refined 0.191 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_other 0.156 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.112 r_chiral_restr 0.077 r_metal_ion_refined 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 2894 Nucleic Acid Atoms 363 Solvent Atoms 359 Heterogen Atoms 3
Software Software Software Name Purpose SHELXCD phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building ARP/wARP model building REFMAC refinement DENZO data reduction SCALEPACK data scaling DM phasing