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Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUE PDB ENTRY 1NUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.2M CaCl2, 0.1M HEPES-Na, pH 7.5, 28% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.85 33.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.28 α = 90 b = 108.7 β = 90 c = 119.65 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 20 99.1 0.09 9.31 2.9 40870 40514 54.98
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) 2.3 2.44 97.2 0.8
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 1NUE 2.35 20 36370 36283 1918 99.76 0.22035 0.22035 0.21668 0.221 0.28944 0.2244 RANDOM 47.772
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] 1.96 1.63 -3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.428 r_scangle_it 3.811 r_scbond_it 2.351 r_angle_refined_deg 1.776 r_mcangle_it 1.527 r_angle_other_deg 0.977 r_mcbond_it 0.84 r_symmetry_hbond_refined 0.326 r_symmetry_vdw_refined 0.307 r_xyhbond_nbd_refined 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.428 r_scangle_it 3.811 r_scbond_it 2.351 r_angle_refined_deg 1.776 r_mcangle_it 1.527 r_angle_other_deg 0.977 r_mcbond_it 0.84 r_symmetry_hbond_refined 0.326 r_symmetry_vdw_refined 0.307 r_xyhbond_nbd_refined 0.254 r_nbd_other 0.247 r_nbd_refined 0.227 r_symmetry_vdw_other 0.203 r_metal_ion_refined 0.154 r_chiral_restr 0.106 r_nbtor_other 0.095 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other 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 7094 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing