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Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EX7 PDB ENTRY 1EX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 292 4% (w/v) PEG 3350, 40mM potassium thiocyanate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.14 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.225 α = 90 b = 68.225 β = 90 c = 151.272 γ = 120
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 MARRESEARCH 2003-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9793 ESRF BM30A
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 2.35 20 99.3 0.071 28.8 12 16498 16498 43.7
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 2.35 2.41 97.7 0.144 16.4 11.8 1172
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-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 1EX7 2.35 19.69 15672 15672 833 99.59 0.18859 0.18859 0.18488 0.194 0.25762 0.1996 RANDOM 17.622
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 r_dihedral_angle_1_deg 6.472 r_scangle_it 3.326 r_scbond_it 2.003 r_angle_refined_deg 1.478 r_mcangle_it 1.222 r_angle_other_deg 0.848 r_mcbond_it 0.636 r_symmetry_vdw_other 0.285 r_nbd_other 0.229 r_symmetry_hbond_refined 0.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.472 r_scangle_it 3.326 r_scbond_it 2.003 r_angle_refined_deg 1.478 r_mcangle_it 1.222 r_angle_other_deg 0.848 r_mcbond_it 0.636 r_symmetry_vdw_other 0.285 r_nbd_other 0.229 r_symmetry_hbond_refined 0.229 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.209 r_symmetry_vdw_refined 0.188 r_metal_ion_refined 0.14 r_nbtor_other 0.085 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3290 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing