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Crystal structure of human ribokinase in complex with AMP
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 8.5 277 0.1M Tris, 8% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.09 α = 90 b = 63.87 β = 90 c = 181.02 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 QUANTUM 315 2008-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 31.5 99.6 0.095 15.1 7.2 44741 25.575
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 2.05 97.2 0.905 2.1 7.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FV7 2 31.5 42440 2232 99.62 0.17704 0.17464 0.22186 0.2027 RANDOM 43.534
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] -0.53 1.45 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.861 r_dihedral_angle_3_deg 14.714 r_dihedral_angle_4_deg 14.414 r_long_range_B_refined 7.094 r_long_range_B_other 7.094 r_dihedral_angle_1_deg 6.405 r_scangle_other 2.659 r_angle_refined_deg 2.124 r_scbond_it 1.736 r_scbond_other 1.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.861 r_dihedral_angle_3_deg 14.714 r_dihedral_angle_4_deg 14.414 r_long_range_B_refined 7.094 r_long_range_B_other 7.094 r_dihedral_angle_1_deg 6.405 r_scangle_other 2.659 r_angle_refined_deg 2.124 r_scbond_it 1.736 r_scbond_other 1.736 r_angle_other_deg 1.595 r_mcangle_it 1.464 r_mcangle_other 1.464 r_mcbond_it 0.936 r_mcbond_other 0.936 r_chiral_restr 0.128 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.009 r_gen_planes_other 0.007 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 4595 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing