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Structure of WSSV thymidylate synthase in complex with dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The protein in complex with dUMP was crystallized in drops containing 1 ul protein solution (10 mg/ml protein + 5 mM dUMP incubated at 4 degrees for 4 h) and 1 ul reservoir solution (100 mM Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 200 mM Li2SO4).
Crystal Properties Matthews coefficient Solvent content 3.18 61.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.91 α = 90 b = 132.35 β = 90 c = 234.11 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 PIXEL DECTRIS PILATUS 6M 2016-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.275 117.054 100 0.07 0.073 0.02 0.999 22.2 13.2 79528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.275 2.282 99 1.159 1.21 0.341 0.902 2 12.4
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 6K7R 2.275 117.054 79438 3955 99.3 0.189 0.188 0.1903 0.208 0.2101 RANDOM 60.93
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] -10.7716 -5.2111 15.9827
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.89 t_omega_torsion 3.45 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.89 t_omega_torsion 3.45 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9026 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 213
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing