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Crystal structure of human glucokinase
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, HANGING DROP 6.6 293 PEG1500, Hepes, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 56.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.855 α = 90 b = 79.855 β = 90 c = 322.221 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 DIFFRACTOMETER WEISSENBERG 2001-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 1.000 Photon Factory BL-6B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 42.42 98.5 0.033 22.1 3.8 27833 -3 29.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 96.1 0.128 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1CZA 2.3 42.42 2 27833 26980 1870 95.5 0.241 0.235 0.232 0.2362 0.273 0.2736 RANDOM 47.7
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] 6.47 4.2 6.47 -12.94
RMS Deviations Key Refinement Restraint Deviation o_dihedral_angle_d 21.9 o_scangle_it 3.24 o_mcangle_it 2.58 o_scbond_it 2.17 o_mcbond_it 1.55 o_angle_deg 1.2 o_improper_angle_d 0.7 o_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3505 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 36
Software Software Software Name Purpose CNX refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing