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T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LTQ PDB ID 1LTQ dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 295 100mM Sodium cacodylate, 12% PEG-8000, 0.2 M ammonium sulfate, 20 mM urea, 5 mM DTT, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.41 63.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.63 α = 90 b = 128.05 β = 90 c = 357.12 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 130 CCD MAR CCD 165 mm Double crystal monochromator with sagitally focusing Si(111) crystals 2002-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 0.979 NSLS X9A
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 2.9 40 98.7 0.104 12.01 4.32 126336 124693 -999 -3 71.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 2.95 0.535 1.57 3.5 6245
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 ID 1LTQ dimer 2.9 19.99 1 126245 111683 2835 88 0.24 0.24 0.23 0.286 0.2774 RANDOM 60.5
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] -1.2 24.83 -23.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 8.81 c_mcangle_it 7.02 c_scbond_it 5.7 c_mcbond_it 4.26 c_angle_deg 2.4 c_improper_angle_d 2.18 c_bond_d 0.151 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 8.81 c_mcangle_it 7.02 c_scbond_it 5.7 c_mcbond_it 4.26 c_angle_deg 2.4 c_improper_angle_d 2.18 c_bond_d 0.151 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 28415 Nucleic Acid Atoms Solvent Atoms 976 Heterogen Atoms 198
Software Software Software Name Purpose CNS refinement CBASS data collection DENZO data reduction SCALEPACK data scaling CNS phasing