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Crystal structure of a UMP/dUMP methylase PolB from Streptomyces cacaoi bound with 5-Br UMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M HEPES, pH 7.5, 10%PEG4000, 5 % isopropanol
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.897 α = 90 b = 94.16 β = 98.3 c = 91.948 γ = 90
Symmetry Space Group P 1 21 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 1.76 50 98.7 13.49 7.5 103864
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 1.76 50 98597 5222 98.41 0.15572 0.15378 0.1568 0.19251 0.1582 RANDOM 19.28
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] 0.63 0.5 -0.33 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.711 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_3_deg 12.733 r_scangle_it 6.163 r_dihedral_angle_1_deg 5.866 r_scbond_it 3.991 r_mcangle_it 2.711 r_angle_refined_deg 2.285 r_mcbond_it 1.617 r_chiral_restr 0.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.711 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_3_deg 12.733 r_scangle_it 6.163 r_dihedral_angle_1_deg 5.866 r_scbond_it 3.991 r_mcangle_it 2.711 r_angle_refined_deg 2.285 r_mcbond_it 1.617 r_chiral_restr 0.423 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 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 7218 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 300
Software Software Software Name Purpose REFMAC refinement