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E134A mutant 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 6.5 293 0.18M CALCIUM ACETATE HYDRATE, 0.09M SODIUM CACODYLATE TRIHYDRATE, 16% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.489 α = 90 b = 93.149 β = 103.6 c = 68.41 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 2.3 90.54 93.8 0.063 16 2.9 47185
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 2.3 2.38 91 0.251 2.9 2.3
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 2.3 22.98 47181 2402 93.2 0.191 0.189 0.1849 0.235 0.2267 RANDOM 28.78
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] -1.81 -1.48 2.45 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 15.089 r_scangle_it 5.288 r_dihedral_angle_1_deg 5.189 r_scbond_it 3.259 r_mcangle_it 2.145 r_angle_refined_deg 1.63 r_mcbond_it 1.194 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 15.089 r_scangle_it 5.288 r_dihedral_angle_1_deg 5.189 r_scbond_it 3.259 r_mcangle_it 2.145 r_angle_refined_deg 1.63 r_mcbond_it 1.194 r_chiral_restr 0.115 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8462 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling