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Crystal Structure of ROK Hexokinase from Thermus thermophilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris-HCl (pH 8.5), 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.926 α = 90 b = 138.144 β = 95.41 c = 75.156 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 QUANTUM 315 2011-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
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 2.02 50 99.7 0.071 11.6 4.4 93722 93458 1 1 26.3
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 2.02 2.09 99.3 0.363 3.22 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.02 33.6 93458 88643 4686 99.6 0.18308 0.18091 0.1798 0.22537 0.2232 RANDOM 32.885
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.537 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 17.579 r_dihedral_angle_1_deg 12.225 r_scangle_it 4.408 r_scbond_it 2.748 r_mcangle_it 1.795 r_angle_refined_deg 1.661 r_mcbond_it 1.537 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.537 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 17.579 r_dihedral_angle_1_deg 12.225 r_scangle_it 4.408 r_scbond_it 2.748 r_mcangle_it 1.795 r_angle_refined_deg 1.661 r_mcbond_it 1.537 r_nbtor_refined 0.307 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.212 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8694 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 34
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling