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EBV dUTPase mutant Asp131Asn with bound dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BSY PDB ENTRY 2BSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.3 M AMMONIUM SULFATE, 25 % PEG 3350, 0.1 M HEPES PH 7, 10 MM DUTP
Crystal Properties Matthews coefficient Solvent content 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.624 α = 90 b = 56.859 β = 90 c = 81.073 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 ADSC CCD TOROIDAL MIRROR 2007-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.38 46.57 98.8 0.08 6.56 3.45 24052 16.4
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 1.8 1.9 99.9 0.35 2.16 3.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BSY 1.8 46.57 22791 1229 98.13 0.1982 0.19562 0.1952 0.2474 0.2473 RANDOM 17.495
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] -0.11 0.23 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.468 r_dihedral_angle_4_deg 18.78 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 5.993 r_scangle_it 4.09 r_scbond_it 2.668 r_mcangle_it 1.716 r_angle_refined_deg 1.632 r_mcbond_it 1.059 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.468 r_dihedral_angle_4_deg 18.78 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 5.993 r_scangle_it 4.09 r_scbond_it 2.668 r_mcangle_it 1.716 r_angle_refined_deg 1.632 r_mcbond_it 1.059 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1936 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing