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Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1 M HEPES/Sodium hydroxide pH 7.5, 0.1 M Sodium chloride, 30 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.682 α = 90 b = 90.682 β = 90 c = 334.933 γ = 120
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 2008-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 20 99.6 0.04 16.62 3.6 84393 84393 16.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 99.9 0.335 3.9 3.57
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.5 19.6 84392 84392 4298 99.64 0.16964 0.16873 0.1931 0.18639 0.211 RANDOM 17.11
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] -0.12 -0.06 -0.12 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.849 r_dihedral_angle_4_deg 15.246 r_dihedral_angle_3_deg 12.661 r_dihedral_angle_1_deg 5.965 r_angle_other_deg 3.95 r_scangle_it 2.663 r_scbond_it 1.693 r_angle_refined_deg 1.207 r_mcangle_it 1.171 r_mcbond_it 0.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.849 r_dihedral_angle_4_deg 15.246 r_dihedral_angle_3_deg 12.661 r_dihedral_angle_1_deg 5.965 r_angle_other_deg 3.95 r_scangle_it 2.663 r_scbond_it 1.693 r_angle_refined_deg 1.207 r_mcangle_it 1.171 r_mcbond_it 0.626 r_symmetry_vdw_refined 0.336 r_symmetry_vdw_other 0.269 r_nbd_other 0.236 r_nbd_refined 0.203 r_nbtor_refined 0.186 r_symmetry_metal_ion_refined 0.149 r_metal_ion_refined 0.147 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.107 r_chiral_restr 0.08 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 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 2982 Nucleic Acid Atoms 405 Solvent Atoms 476 Heterogen Atoms 23
Software Software Software Name Purpose MxCuBE data collection SHELXCD phasing SHELXD phasing SHELXE model building ARP/wARP model building REFMAC refinement XDS data reduction XSCALE data scaling