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Adenylate kinase from Methanococcus voltae
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 4.6 298 PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal Properties Matthews coefficient Solvent content 5.25 76.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.5 α = 90 b = 200.5 β = 90 c = 200.5 γ = 90
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 MARRESEARCH bent conical Si-mirror (Rh coating) 1999-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.037 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 87.4 46286 39038 29.9
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 2.5 33.42 39038 39001 3917 84.2 0.2201 0.2201 0.22 0.2197 0.253 0.2519 RANDOM
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 c_dihedral_angle_d 21.8 c_scangle_it 2.24 c_mcangle_it 2.21 c_scbond_it 1.42 c_angle_deg 1.3 c_mcbond_it 1.22 c_improper_angle_d 0.77 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4419 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 46
Software Software Software Name Purpose XDS data reduction AMoRE phasing CNS refinement XDS data scaling