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Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum in complex with CDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.2M MgCl2, 0.1M HEPES-Na, pH7.5, 30% PEG 400, 10mM Co(NH3)6Cl3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.37 α = 90 b = 71.52 β = 95.53 c = 157.99 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 MARRESEARCH 2005-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.2 20 80.3 0.063 10.14 2.7 70403 56525 45.36
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) 2.2 2.3 64.9 0.289 3.32
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 1nue 2.2 20 53700 53700 2824 80.43 0.2032 0.2032 0.19964 0.2065 0.27074 0.2046 RANDOM 37.966
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] -0.09 -0.29 0.59 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.651 r_scangle_it 4.064 r_scbond_it 2.542 r_angle_refined_deg 1.934 r_mcangle_it 1.605 r_angle_other_deg 0.977 r_mcbond_it 0.896 r_symmetry_vdw_other 0.325 r_nbd_other 0.25 r_symmetry_vdw_refined 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.651 r_scangle_it 4.064 r_scbond_it 2.542 r_angle_refined_deg 1.934 r_mcangle_it 1.605 r_angle_other_deg 0.977 r_mcbond_it 0.896 r_symmetry_vdw_other 0.325 r_nbd_other 0.25 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.176 r_chiral_restr 0.113 r_nbtor_other 0.096 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10750 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 227
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing