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Crystal structure of E. coli Adenylate kinase R119A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 PURIFIED ADK IN 50 MM NACL AND 30 MM
MES BUFFER, PH 6.0 WAS CONCENTRATED TO 18 MG/ML AND CO- CRYSTALLIZED WITH A 5 MOLAR EXCESS OF AP5A. A TYPICAL DROP CONTAINED 2 MICROL OF PROTEIN MIXED WITH 2 MICROL OF PRECIPITANT
AND EQUILIBRATED AGAINST 1 ML RESERVOIR SOLUTION CONTAINING 28-30% PEG 4K, 0.2 M MgCL2 AND 0.1 M Tris-HCl, PH 8.5).
Crystal Properties Matthews coefficient Solvent content 2.23 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.314 α = 90 b = 31.503 β = 110.93 c = 53.189 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.69 48.221 99.9 0.122 0.09 0.994 7.2 4.7 22857
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 0.824 0.568 0.598 1.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4x8h 1.69 48.221 22857 1915 96.32 0.1865 0.1819 0.1825 0.235 0.2317
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 f_dihedral_angle_d 12.847 f_angle_d 0.863 f_chiral_restr 0.05 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1649 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing