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Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LQM PDB ENTRY 1LQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 HANGING DROP VAPOUR DIFFUSION METHOD. PROTEIN IN 100 MM NACL, 20 MM TRIS-HCL PH 7.5 AND 10 MM DTT AT 30 TO 50 MG/ML. RESERVOIR SOLUTION OF 20% PEG 3350 AND 0.05 M NH4CL.
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.406 α = 90 b = 82.942 β = 90 c = 269.13 γ = 90
Symmetry Space Group C 2 2 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 MARRESEARCH TOROIDAL MIRROR 2004-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.3 67.3 92.3 0.1 5.4 5.81 29123
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 2.3 2.42 90.5 0.35 2.16 5.84
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 1LQM 2.3 49.88 27583 1482 92 0.196 0.193 0.1879 0.257 0.2502 RANDOM 24.17
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] 0.06 0.21 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.584 r_dihedral_angle_3_deg 14.561 r_dihedral_angle_4_deg 14.498 r_dihedral_angle_1_deg 4.748 r_mcangle_it 4.302 r_scangle_it 3.186 r_mcbond_it 3.169 r_scbond_it 2.382 r_angle_refined_deg 0.829 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.584 r_dihedral_angle_3_deg 14.561 r_dihedral_angle_4_deg 14.498 r_dihedral_angle_1_deg 4.748 r_mcangle_it 4.302 r_scangle_it 3.186 r_mcbond_it 3.169 r_scbond_it 2.382 r_angle_refined_deg 0.829 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.235 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.06 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 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 4910 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing