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Crystal Structure Of Unliganded Form Of Oligomeric E.coli Guanylate Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AN9 PDB ID 2AN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 16% (w/v) PEG 10000, 0.08M sodium hepes, 0.1M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.8 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.238 α = 90 b = 108.238 β = 90 c = 273.992 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 CCD ADSC QUANTUM 4 2003-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 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 3.2 34 99.7 0.071 26.9 10.6 27681 27681 58.3
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) 3.2 3.28 99.7 0.225 11.6 11 1974
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 ID 2AN9 3.2 33.9 26296 26296 1397 99.9 0.25722 0.25722 0.25583 0.2532 0.28298 0.2591 RANDOM 74.42
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_2_deg 37.521 r_dihedral_angle_3_deg 17.89 r_dihedral_angle_4_deg 15.561 r_mcangle_it 9.925 r_mcbond_it 7.647 r_dihedral_angle_1_deg 4.095 r_angle_refined_deg 1.1 r_scangle_it 1.03 r_scbond_it 0.715 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.521 r_dihedral_angle_3_deg 17.89 r_dihedral_angle_4_deg 15.561 r_mcangle_it 9.925 r_mcbond_it 7.647 r_dihedral_angle_1_deg 4.095 r_angle_refined_deg 1.1 r_scangle_it 1.03 r_scbond_it 0.715 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 9413 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing