☰ Navigation Tabs
Crystal Structure of E.coli Dha kinase DhaK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OI2 pdb entry 1OI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295 20% PEG 8000, 0.1M Sodium Citrate pH 5.6, vapor diffusion, sitting drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.18 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.833 α = 90 b = 91.507 β = 89.96 c = 73.232 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 2008-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.21 49.83 93.3 0.122 9.5 5.2 30618
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 2.21 2.29 81.1 0.457 2.7 2634
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 1OI2 2.21 49.83 30579 1561 93 0.1738 0.1719 0.1727 0.2099 0.2093 RANDOM 30.6636
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] -0.19 -0.01 -0.56 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.59 r_dihedral_angle_4_deg 20.742 r_dihedral_angle_3_deg 15.709 r_dihedral_angle_1_deg 6.351 r_scangle_it 2.839 r_scbond_it 1.78 r_angle_refined_deg 1.354 r_mcangle_it 1.081 r_mcbond_it 0.635 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.59 r_dihedral_angle_4_deg 20.742 r_dihedral_angle_3_deg 15.709 r_dihedral_angle_1_deg 6.351 r_scangle_it 2.839 r_scbond_it 1.78 r_angle_refined_deg 1.354 r_mcangle_it 1.081 r_mcbond_it 0.635 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5308 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing