☰ Navigation Tabs
Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Imidazole, PEG1000, Calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.38 48.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.041 α = 103.43 b = 72.128 β = 94.96 c = 115.994 γ = 99.48
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 AGILENT EOS CCD 2010-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 50 98.6 14.42 4 109477
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.19 46.2 99716 5226 98.6 0.18724 0.1846 0.1898 0.23776 0.241 RANDOM 33.575
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] -0.04 -0.02 0.01 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.922 r_dihedral_angle_4_deg 22.536 r_dihedral_angle_3_deg 18.872 r_dihedral_angle_1_deg 7.601 r_long_range_B_refined 6.553 r_long_range_B_other 6.553 r_scangle_other 5.175 r_mcangle_it 3.553 r_mcangle_other 3.552 r_scbond_it 3.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.922 r_dihedral_angle_4_deg 22.536 r_dihedral_angle_3_deg 18.872 r_dihedral_angle_1_deg 7.601 r_long_range_B_refined 6.553 r_long_range_B_other 6.553 r_scangle_other 5.175 r_mcangle_it 3.553 r_mcangle_other 3.552 r_scbond_it 3.289 r_scbond_other 3.289 r_mcbond_it 2.37 r_mcbond_other 2.37 r_angle_refined_deg 1.418 r_angle_other_deg 0.496 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15585 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing