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Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JAS PDB ENTRY 2JAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 20% PEG 3350, 0.2 M MGCL2, pH 5.90
Crystal Properties Matthews coefficient Solvent content 2.2 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.931 α = 90 b = 83.931 β = 90 c = 53.31 γ = 120
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 2006-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.6 43 98 0.04 22.7 3.9 11196 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 2.6 2.74 99.6 0.3 4.1 3.9
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 2JAS 2.6 25 12030 632 98.1 0.224 0.222 0.2201 0.266 0.2688 RANDOM 38.59
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] 0.41 0.2 0.41 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 19.325 r_dihedral_angle_3_deg 17.712 r_dihedral_angle_1_deg 5.822 r_scangle_it 1.902 r_angle_refined_deg 1.269 r_scbond_it 1.156 r_mcangle_it 0.826 r_mcbond_it 0.466 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 19.325 r_dihedral_angle_3_deg 17.712 r_dihedral_angle_1_deg 5.822 r_scangle_it 1.902 r_angle_refined_deg 1.269 r_scbond_it 1.156 r_mcangle_it 0.826 r_mcbond_it 0.466 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.086 r_bond_refined_d 0.01 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_refined 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 3197 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing