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Activation of Ribokinase by Monovalent Cations
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 CRYSTALS WERE GROWN IN DROPS CONTAINING 0.3 MM WILD-TYPE RK, 5 MM D-RIBOSE, 10 MM AMP-PCP, 75 MM MGCL2, 60 MM CSCL, 10% 2-METHYL-2,4-PENTANEDIOL, 10% POLYETHYLENE GLYCOL 4000 AND 50 MM SODIUM ACETATE, PH 4.8.
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.453 α = 90 b = 62.767 β = 90 c = 339.277 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 MARRESEARCH 2000-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.34 17 98.2 0.091 10.9 4.9 50296
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) 1 2.34 2.38 99.9 0.377 3.8
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 OTHER THROUGHOUT 2.34 17 50296 2480 98.2 0.196 0.193 0.1948 0.257 0.2564 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.007 r_scbond_it 5.394 r_mcangle_it 3.154 r_mcbond_it 1.924 r_angle_other_deg 1.574 r_nbd_refined 0.268 r_symmetry_vdw_refined 0.254 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.148
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.007 r_scbond_it 5.394 r_mcangle_it 3.154 r_mcbond_it 1.924 r_angle_other_deg 1.574 r_nbd_refined 0.268 r_symmetry_vdw_refined 0.254 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.148 r_chiral_restr 0.114 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_refined_deg r_dihedral_angle_1_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_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 8976 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling