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nucleoside diphosphate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 6000, magnesium chloride,Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.66 53.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.633 α = 90 b = 76.633 β = 90 c = 106.51 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH mirrors 2003-03-15 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 0.9754 LURE DW32
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 24.71 98.4 0.074 0.074 18.7 23 5418 5418 40
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 97.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.7 24.71 4823 4823 595 98.42 0.1878 0.18787 0.18215 0.1806 0.23216 0.2204 RANDOM 37.258
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] 1.14 0.57 1.14 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.445 r_angle_refined_deg 1.544 r_angle_other_deg 0.958 r_symmetry_vdw_other 0.256 r_nbd_other 0.226 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.105 r_nbtor_other 0.094 r_symmetry_hbond_refined 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.445 r_angle_refined_deg 1.544 r_angle_other_deg 0.958 r_symmetry_vdw_other 0.256 r_nbd_other 0.226 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.105 r_nbtor_other 0.094 r_symmetry_hbond_refined 0.076 r_symmetry_vdw_refined 0.065 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1127 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHARP phasing