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Structure of human ribokinase crystallized with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 0.1M sodium HEPES, 7% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.58 52.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.31 α = 90 b = 168.14 β = 90.82 c = 161.5 γ = 90
Symmetry Space Group P 1 21 1
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 2010-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.1 NSLS X12C
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 2.6 51.26 99.7 0.135 9 3.8 130659 21.521
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 2.6 2.67 97.3 0.703 2 3.8
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 2FV7 2.6 51.26 124139 6493 99.66 0.20609 0.2047 0.2087 0.23205 0.2343 RANDOM 39.583
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] -2.05 0.21 0.58 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 15.833 r_dihedral_angle_1_deg 6.081 r_long_range_B_refined 3.806 r_long_range_B_other 3.806 r_angle_other_deg 2.117 r_angle_refined_deg 1.903 r_scangle_other 1.419 r_mcangle_it 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 15.833 r_dihedral_angle_1_deg 6.081 r_long_range_B_refined 3.806 r_long_range_B_other 3.806 r_angle_other_deg 2.117 r_angle_refined_deg 1.903 r_scangle_other 1.419 r_mcangle_it 1.022 r_mcangle_other 1.022 r_scbond_it 0.907 r_scbond_other 0.907 r_mcbond_it 0.582 r_mcbond_other 0.582 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_bond_other_d 0.015 r_gen_planes_refined 0.013 r_gen_planes_other 0.011 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27417 Nucleic Acid Atoms Solvent Atoms 810 Heterogen Atoms 348
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing