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Crystal structure of human N-acetylglucosamine kinase in complex with N-acetylglucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other HUMAN N-ACETYLGLUCOSAMINE KINASE IN COMPLEX WITH ADP AND GLUCOSE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 100 MM HEPES PH 7.0, 100 MM NACL, 8% (W/V) PEG 4000, 2MM GLCNAC
Crystal Properties Matthews coefficient Solvent content 3.3 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.537 α = 63.43 b = 98.482 β = 75.66 c = 101.981 γ = 75.06
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 2005-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.9 2.05 93.3 0.05 16.8 1.7 140534 2.5
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 1.9 2.05 81.2 0.32 2.5 1.4
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 HUMAN N-ACETYLGLUCOSAMINE KINASE IN COMPLEX WITH ADP AND GLUCOSE 1.9 90.17 137744 2817 93.3 0.167 0.167 0.1768 0.199 0.2076 RANDOM 24.16
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] -0.01 0.04 -1.37 -0.18 0.83 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.889 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 6.032 r_scangle_it 3.228 r_scbond_it 2.277 r_angle_refined_deg 1.361 r_mcangle_it 1.291 r_mcbond_it 1.081 r_angle_other_deg 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.889 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 6.032 r_scangle_it 3.228 r_scbond_it 2.277 r_angle_refined_deg 1.361 r_mcangle_it 1.291 r_mcbond_it 1.081 r_angle_other_deg 0.83 r_symmetry_vdw_other 0.3 r_nbd_refined 0.228 r_nbd_other 0.191 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.156 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 10482 Nucleic Acid Atoms Solvent Atoms 1272 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing