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Structure of Mouse ADP-Dependent Glucokinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UA4 PDB entries 1UA4, 1L2L, & 1GC5 experimental model PDB 1L2L PDB entries 1UA4, 1L2L, & 1GC5 experimental model PDB 1GC5 PDB entries 1UA4, 1L2L, & 1GC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.2 M NH4Cl, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.923 α = 90 b = 58.686 β = 90 c = 160.942 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 CCD ADSC QUANTUM 315 2012-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9184 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.094 47.416 99.8 0.12 0.12 9.3 4.8 26310 26310 19.2
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 2.1 2.16 100 0.76 2 4.9
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 PDB entries 1UA4, 1L2L, & 1GC5 2.1 47.4 24797 1318 99.54 0.19557 0.19299 0.2023 0.24416 0.2519 RANDOM 36.201
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] 1.28 -0.06 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.828 r_dihedral_angle_4_deg 14.106 r_dihedral_angle_3_deg 13.52 r_long_range_B_refined 6.609 r_long_range_B_other 6.541 r_dihedral_angle_1_deg 6.118 r_scangle_other 4.171 r_mcangle_it 3.613 r_mcangle_other 3.612 r_scbond_it 2.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.828 r_dihedral_angle_4_deg 14.106 r_dihedral_angle_3_deg 13.52 r_long_range_B_refined 6.609 r_long_range_B_other 6.541 r_dihedral_angle_1_deg 6.118 r_scangle_other 4.171 r_mcangle_it 3.613 r_mcangle_other 3.612 r_scbond_it 2.642 r_scbond_other 2.641 r_mcbond_it 2.301 r_mcbond_other 2.299 r_angle_refined_deg 1.273 r_angle_other_deg 0.881 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 3439 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building