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Adenylate kinase from Methanococcus thermolithotrophicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKS PDB entry 1NKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 6000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal Properties Matthews coefficient Solvent content 2.8 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.5 α = 90 b = 128.5 β = 90 c = 88.5 γ = 90
Symmetry Space Group P 4 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 IV confocal 1999-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2.5 50 94.7 0.068 27043 25623 32.7
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 1NKS 2.76 30.78 18370 18370 1812 94 0.2041 0.2041 0.204 0.2043 0.287 0.2864 RANDOM 43
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] 2.83 2.83 -5.66
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.7 c_scangle_it 4.88 c_mcangle_it 3.79 c_scbond_it 3.42 c_mcbond_it 2.35 c_angle_deg 1.3 c_improper_angle_d 0.76 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4498 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose Crystal data collection d*TREK data reduction AMoRE phasing CNS refinement CrystalClear data reduction d*TREK data scaling