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Crystal structure of wild-type adenylate kinase from E. coli, in complex with Ap5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKE PDB entry 1AKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 45 mg/ml AK in 50 mM MES pH 6.7, 1 mM EDTA, with 50% 50mM MES pH 7.0-7.3, 3% w/v PEG 2000 and 1.8-2.3 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.646 α = 90 b = 72.639 β = 90 c = 78.699 γ = 90
Symmetry Space Group P 21 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 MACSCIENCE 2008-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 1.5418
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 1.9 50 98.2 0.046 47.55 4.9 36651
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 1.9 2.03 82.8 0.159 9.06 3048
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1AKE 2 14.999 32979 3277 99.93 0.204 0.1994 0.2454 0.2496 RANDOM 34.33
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] 0.4442 0.0313 -0.4755
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.879 f_angle_d 1.511 f_chiral_restr 0.052 f_bond_d 0.011 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3312 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms 114
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement DENZO data reduction SCALEPACK data scaling