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Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside 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 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.07 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.5 α = 90 b = 70.82 β = 90.1 c = 226.032 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 ADSC CCD 2005-06-12 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 2.9 50 97.3 0.11 13 3.7 50991 2
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 2.9 3.06 97.1 0.46 2.1 3.8
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 1J90 2.9 30 45938 2468 97 0.25 0.248 0.287 0.2252 RANDOM 45.8
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] -2.45 -1.37 3.03 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.283 r_dihedral_angle_3_deg 18.509 r_dihedral_angle_4_deg 13.118 r_dihedral_angle_1_deg 5.91 r_scangle_it 2.212 r_angle_refined_deg 1.425 r_scbond_it 1.327 r_mcangle_it 1.195 r_mcbond_it 0.651 r_symmetry_vdw_refined 0.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.283 r_dihedral_angle_3_deg 18.509 r_dihedral_angle_4_deg 13.118 r_dihedral_angle_1_deg 5.91 r_scangle_it 2.212 r_angle_refined_deg 1.425 r_scbond_it 1.327 r_mcangle_it 1.195 r_mcbond_it 0.651 r_symmetry_vdw_refined 0.348 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12847 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing