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Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 0.1 M MES/Sodium hydroxide pH 6.5, 0.1 M Sodium chloride, 0.1 M Lithium sulfate, 30 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.089 α = 90 b = 90.089 β = 90 c = 334.254 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 2008-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.97982 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 1.75 20 96.8 0.066 13.52 3.99 51564 51564 22.6
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 1.75 1.8 99.1 0.4 4.48 3.95 3874
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 SAD THROUGHOUT 1.75 19.71 51564 51564 2654 96.86 0.18212 0.18212 0.18084 0.2013 0.20533 0.2244 RANDOM 21.338
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] 0.88 0.44 0.88 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.996 r_dihedral_angle_4_deg 20.812 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 5.633 r_angle_other_deg 3.917 r_scangle_it 2.662 r_scbond_it 1.745 r_mcangle_it 1.263 r_angle_refined_deg 1.224 r_mcbond_it 0.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.996 r_dihedral_angle_4_deg 20.812 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 5.633 r_angle_other_deg 3.917 r_scangle_it 2.662 r_scbond_it 1.745 r_mcangle_it 1.263 r_angle_refined_deg 1.224 r_mcbond_it 0.687 r_symmetry_vdw_other 0.304 r_symmetry_vdw_refined 0.296 r_nbd_other 0.238 r_nbd_refined 0.205 r_nbtor_refined 0.187 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.135 r_metal_ion_refined 0.111 r_nbtor_other 0.106 r_chiral_restr 0.077 r_symmetry_metal_ion_refined 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 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 2974 Nucleic Acid Atoms 363 Solvent Atoms 394 Heterogen Atoms 20
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