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Structure of deoxyadenosine kinase from M.mycoides with bound dATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5Z PDB ENTRY 1P5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 24% PEG 3350 0.2 M KSCN, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.845 α = 90 b = 100.85 β = 124.58 c = 109.486 γ = 90
Symmetry Space Group C 1 2 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 MIRROR 2004-09-25 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 2.7 47.1 100 0.08 15.6 3.6 46941 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 2.7 2.85 100 0.4 2.9 3.7
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 THROUGHOUT PDB ENTRY 1P5Z 2.7 47 44555 2372 99.7 0.235 0.233 0.2331 0.274 0.2712 RANDOM 40.39
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] -1.26 -0.53 2.2 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.548 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 17.323 r_dihedral_angle_1_deg 5.14 r_angle_refined_deg 1.143 r_scangle_it 1.058 r_scbond_it 0.654 r_mcangle_it 0.536 r_nbtor_refined 0.304 r_mcbond_it 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.548 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 17.323 r_dihedral_angle_1_deg 5.14 r_angle_refined_deg 1.143 r_scangle_it 1.058 r_scbond_it 0.654 r_mcangle_it 0.536 r_nbtor_refined 0.304 r_mcbond_it 0.301 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 9715 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing