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Crystal Structure of Human Deoxyguanosine Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J90 PDB ENTRY 1J90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 287 PEG 4000, AMMONIUM ACETATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.18 α = 90 b = 120.03 β = 90.68 c = 154.35 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 100 CCD MARRESEARCH 1999-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.8 30 97.5 0.112 8.2 3.5 61311 2.2 48
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) 2.8 2.98 95.8 0.318 2.2 2.6
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1J90 2.8 30 59741 3013 97.5 0.265 0.265 0.2845 0.277 RANDOM 43.5
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 2.81 c_mcangle_it 2.34 c_scbond_it 1.71 c_angle_deg 1.4 c_mcbond_it 1.3 c_improper_angle_d 0.88 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 2.81 c_mcangle_it 2.34 c_scbond_it 1.71 c_angle_deg 1.4 c_mcbond_it 1.3 c_improper_angle_d 0.88 c_bond_d 0.008 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 15392 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 240
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling