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Crystal structure of human hexokinase II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CZA pdb entry 1cza
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 16% PEG3350, 0.2M sodium malonate, 0.1M BTP, 10% ethylene glycol, 0.001M DDT, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3 58 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.89 α = 90 b = 129.338 β = 90 c = 187.232 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2006-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 2.45 30 99.8 0.082 15.3 5.5 85698
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) 2.45 2.54 100 0.671 4.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 1cza 2.45 25 83669 2083 98.172 0.232 0.2301 0.2344 0.287 0.2881 thin shells 42.349
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] 1.448 -2.777 1.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_3_deg 15.766 r_dihedral_angle_1_deg 6.447 r_scangle_it 2.336 r_scbond_it 1.493 r_angle_refined_deg 1.427 r_angle_other_deg 1.349 r_mcangle_it 1.18 r_scangle_other 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_3_deg 15.766 r_dihedral_angle_1_deg 6.447 r_scangle_it 2.336 r_scbond_it 1.493 r_angle_refined_deg 1.427 r_angle_other_deg 1.349 r_mcangle_it 1.18 r_scangle_other 1.12 r_mcbond_it 0.713 r_scbond_other 0.665 r_mcangle_other 0.587 r_symmetry_vdw_other 0.333 r_nbd_refined 0.215 r_nbd_other 0.204 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.147 r_nbtor_other 0.094 r_chiral_restr 0.08 r_mcbond_other 0.072 r_bond_refined_d 0.017 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13309 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 140
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building PRODRG refinement MolProbity model building