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Crystal structure of S. aureus thymidylate kinase complexed with thymidine monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CCG PDB ENTRY 2CCG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 1M LICL, 0.1M NA CACODYLATE PH 7.2, 18% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.17 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.74 α = 90 b = 90.13 β = 100.5 c = 50.25 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE MARRESEARCH MIRRORS 2005-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.7 30 99.4 0.04 43.9 4.7 43797 21.7
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 1.7 1.76 99.4 0.21 7.1 4.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CCG 1.7 20.86 43780 2190 99.3 0.182 0.182 0.221 0.227 RANDOM 26.3
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] 2.34 5.65 -4.86 2.52
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 7.53 c_scbond_it 5.19 c_mcangle_it 3.53 c_mcbond_it 2.79 c_angle_deg 1.3 c_improper_angle_d 0.97 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 7.53 c_scbond_it 5.19 c_mcangle_it 3.53 c_mcbond_it 2.79 c_angle_deg 1.3 c_improper_angle_d 0.97 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 80
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing