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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 5.6 293 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE TRIBASIC DEHYDRATE, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.02 75.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.531 α = 90 b = 112.531 β = 90 c = 125.981 γ = 120
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 ADSC QUANTUM 4r 2008-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A
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 77.08 97.3 0.046 26 4.1 25691
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 92.1 0.33 2.4 2.6
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 35.35 25691 1303 97.3 0.265 0.263 0.2611 0.289 0.2855 RANDOM 48.12
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] 1.72 0.86 1.72 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_4_deg 18.889 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_1_deg 5.671 r_scangle_it 2.528 r_scbond_it 1.397 r_mcangle_it 1.141 r_angle_refined_deg 1.129 r_mcbond_it 0.608 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_4_deg 18.889 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_1_deg 5.671 r_scangle_it 2.528 r_scbond_it 1.397 r_mcangle_it 1.141 r_angle_refined_deg 1.129 r_mcbond_it 0.608 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 2128 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling