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Crystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.33 277 NANODROP, 7.5% 2-propanol, 20.0% polyethylene glycol 4000, 0.1M HEPES pH 7.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.44 α = 90 b = 85.85 β = 90 c = 152.81 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD FLAT MIRROR (VERTICAL FOCUSING) 2006-12-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97899, 0.97935 SSRL BL11-1
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 2.2 28.62 88.9 0.049 11.63 3.97 46716 45.5
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 2.2 2.28 86.2 0.378 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.2 28.62 46612 2367 91.8 0.185 0.182 0.1898 0.232 0.2415 RANDOM 41.37
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] 0.04 -0.24 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.97 r_dihedral_angle_4_deg 17.107 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_1_deg 7.312 r_scangle_it 6.304 r_scbond_it 4.888 r_mcangle_it 2.961 r_mcbond_it 1.938 r_angle_refined_deg 1.565 r_angle_other_deg 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.97 r_dihedral_angle_4_deg 17.107 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_1_deg 7.312 r_scangle_it 6.304 r_scbond_it 4.888 r_mcangle_it 2.961 r_mcbond_it 1.938 r_angle_refined_deg 1.565 r_angle_other_deg 0.848 r_mcbond_other 0.454 r_nbd_refined 0.218 r_symmetry_vdw_other 0.195 r_nbd_other 0.183 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6629 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 69
Software Software Software Name Purpose MolProbity model building SOLVE phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction