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Crystal structure of mouse guanylate kinase in complex with GMP and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 protein solution: 10 mg/ml mGMPK, 2mM GMP, 2mM ADP and 5mM MgCl2
reservoir solution: 38-46% PEG 4000, 0.1M Na-citrate pH 5.6, 0.1-0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.8 56.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.241 α = 90 b = 67.241 β = 90 c = 108.696 γ = 90
Symmetry Space Group P 41 21 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 IMAGE PLATE RIGAKU RAXIS II mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1EX7 2.1 20 15170 14942 1451 98.5 0.188 0.1858 0.231 0.1849 random
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 c_angle_deg 1.53825 c_bond_d 0.011643 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.53825 c_bond_d 0.011643 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 52
Software Software Software Name Purpose XDS data reduction AMoRE phasing CNS refinement XDS data scaling