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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 10% PEG3500, 0.15 M MGAC
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.123 α = 90 b = 148.081 β = 90 c = 41.122 γ = 90
Symmetry Space Group P 21 21 2
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 MAX II BEAMLINE I711 MAX II I711
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 1.7 50 100 0.04 41.5 15.7 44110 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 1.7 74.54 41803 2221 99.9 0.235 0.234 0.2504 0.253 0.2657 RANDOM 23.99
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] -1.13 -1.1 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.172 r_scangle_it 2.51 r_scbond_it 1.57 r_angle_refined_deg 1.247 r_mcangle_it 1.134 r_angle_other_deg 0.751 r_mcbond_it 0.637 r_symmetry_vdw_other 0.315 r_symmetry_vdw_refined 0.246 r_nbd_other 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.172 r_scangle_it 2.51 r_scbond_it 1.57 r_angle_refined_deg 1.247 r_mcangle_it 1.134 r_angle_other_deg 0.751 r_mcbond_it 0.637 r_symmetry_vdw_other 0.315 r_symmetry_vdw_refined 0.246 r_nbd_other 0.233 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.129 r_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 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_refined r_metal_ion_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 2358 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling