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Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BHN PDB ENTRY 1BHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 100mM HEPES-NaOH, 25% PEG400, 10mM EDTA, pH7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.571 α = 90 b = 73.571 β = 90 c = 214.271 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 210 2006-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.59 50 95.7 0.084 30.7 20457
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 1BHN 2.59 47.57 18544 990 95.71 0.22524 0.2218 0.2132 0.2894 0.2754 RANDOM 46.978
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] -0.1 -0.05 -0.1 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.571 r_dihedral_angle_4_deg 25.353 r_dihedral_angle_3_deg 18.473 r_dihedral_angle_1_deg 5.839 r_scangle_it 1.694 r_angle_refined_deg 1.238 r_scbond_it 1.07 r_mcangle_it 0.778 r_mcbond_it 0.449 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.571 r_dihedral_angle_4_deg 25.353 r_dihedral_angle_3_deg 18.473 r_dihedral_angle_1_deg 5.839 r_scangle_it 1.694 r_angle_refined_deg 1.238 r_scbond_it 1.07 r_mcangle_it 0.778 r_mcbond_it 0.449 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.272 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.096 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_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 4894 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing