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Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 15% PEG4000, 0.10 M MGCL2, 0.1 M TRIS-HCL PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.006 α = 90 b = 83.131 β = 90 c = 146.784 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.93 20 97 0.06 20 13.7 58526 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.92 72.55 55509 2955 97.1 0.245 0.243 0.2399 0.281 0.279 RANDOM 21.37
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] 0.39 1.26 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.538 r_scangle_it 2.989 r_scbond_it 2.072 r_angle_refined_deg 1.7 r_mcangle_it 1.264 r_mcbond_it 0.758 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.538 r_scangle_it 2.989 r_scbond_it 2.072 r_angle_refined_deg 1.7 r_mcangle_it 1.264 r_mcbond_it 0.758 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4731 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing