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Crystal structure of a UMP/dUMP methylase PolB from Streptomyces cacaoi bound with 5-Br dUMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium cacodylate, pH 6.5 and 1.4M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.788 α = 90 b = 59.502 β = 120.31 c = 118.981 γ = 90
Symmetry Space Group C 1 2 1
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 225 mm CCD 2009-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9798 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.274 50 98 11 2.9 46721
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 THROUGHOUT 2.274 50 44323 2330 97.58 0.1666 0.16398 0.1633 0.21554 0.2117 RANDOM 30.869
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] -0.96 -0.68 -0.1 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.613 r_dihedral_angle_4_deg 19.89 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_1_deg 6.868 r_scangle_it 5.311 r_scbond_it 3.429 r_mcangle_it 2.104 r_angle_refined_deg 2.102 r_mcbond_it 1.136 r_chiral_restr 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.613 r_dihedral_angle_4_deg 19.89 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_1_deg 6.868 r_scangle_it 5.311 r_scbond_it 3.429 r_mcangle_it 2.104 r_angle_refined_deg 2.102 r_mcbond_it 1.136 r_chiral_restr 0.304 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7382 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 301
Software Software Software Name Purpose REFMAC refinement