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Staphylococcus bacteriophage 80alpha dUTPase with dUMP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 60% ethanol, 0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87 α = 90 b = 87 β = 90 c = 87 γ = 90
Symmetry Space Group P 21 3
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 QUANTUM 315r 2010-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98 ESRF ID23-1
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 2.33 61.52 99.9 0.031 16.2 11 9645
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 2.33 2.46 100 0.1 6.2 10.6
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 3zez 2.33 61.52 9080 541 99.74 0.20322 0.20099 0.2066 0.24437 0.256 RANDOM 38.035
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.704 r_dihedral_angle_3_deg 16.871 r_dihedral_angle_4_deg 15.726 r_dihedral_angle_1_deg 7.03 r_long_range_B_other 6.499 r_long_range_B_refined 6.493 r_scangle_other 4.905 r_mcangle_it 3.754 r_mcangle_other 3.753 r_scbond_it 3.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.704 r_dihedral_angle_3_deg 16.871 r_dihedral_angle_4_deg 15.726 r_dihedral_angle_1_deg 7.03 r_long_range_B_other 6.499 r_long_range_B_refined 6.493 r_scangle_other 4.905 r_mcangle_it 3.754 r_mcangle_other 3.753 r_scbond_it 3.081 r_scbond_other 3.079 r_mcbond_it 2.466 r_mcbond_other 2.457 r_angle_refined_deg 1.633 r_angle_other_deg 0.973 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1289 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing MOSFLM data reduction