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Crystal structure of thymidylate synthase from shrimp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 ul protein solution (20 mg/ml in 10 mM HEPES, 150 mM NaCl, 1 mM DTT, pH 7.5) and 1 ul reservoir solution containing 18% (w/v) PEG 3350, 200 mM (NH4)2SO4, 100 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.27 α = 77.4 b = 103.458 β = 84.81 c = 125.768 γ = 61.43
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 315 2015-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97931 SSRF BL17U1
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 2.269 122.723 97.1 0.054 0.076 0.054 0.99 9.3 2 200394 40.11
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 2.269 2.277 80.1 0.277 0.391 0.276 0.91 2.8 2
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 FREE R-VALUE 1HVY 2.27 89.03 198472 10707 96.2 0.219 0.218 0.2268 0.236 0.24 thin shells 40.68
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] -4.4724 6.1223 -0.7791 0.7059 -0.2059 3.7664
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.54 t_omega_torsion 2.96 t_angle_deg 1.1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.54 t_omega_torsion 2.96 t_angle_deg 1.1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 34386 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 90
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing