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Wild-type nucleoside diphosphate kinase derived from Halomonas sp. 593
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NHK PDB ENTRY 1NHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.19M SODIUM ACETATE, 0.09M TRIS HYDROCHLORIDE, 28% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.974976 79.414146
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.119 α = 90 b = 170.64 β = 93.45 c = 77.636 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 CCD RIGAKU JUPITER 210 2008-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 SPring-8 BL38B1
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 2.7 23.268 91.3 0.047 17.1 1.6 49180
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 2.7 2.8 82.3 0.277 1.7 1.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NHK 2.7 23.268 47868 2404 97.3 0.287 0.287 0.2876 0.314 0.2913 RANDOM 63.98
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] 9.47 5.035 4.34 -13.81
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.875 c_mcangle_it 2.252 c_scbond_it 1.865 c_angle_deg 1.34 c_mcbond_it 1.329 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.875 c_mcangle_it 2.252 c_scbond_it 1.865 c_angle_deg 1.34 c_mcbond_it 1.329 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5320 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling