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Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers
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 7.5 277 0.1M sodium HEPES, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.95 α = 90 b = 89.19 β = 98.16 c = 144.4 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 2009-06-16 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 1.95 44.55 99.8 0.096 11.1 3.8 94826 13.018
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 1.95 2 98.8 0.727 1.9 3.7
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 1.95 44.55 89981 4824 99.75 0.17394 0.17215 0.1816 0.20733 0.2156 RANDOM 30.604
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] 0.87 -0.22 -0.18 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.473 r_dihedral_angle_4_deg 18.055 r_dihedral_angle_3_deg 12.84 r_long_range_B_refined 6.491 r_dihedral_angle_1_deg 6.349 r_long_range_B_other 6.304 r_angle_other_deg 2.073 r_angle_refined_deg 2.011 r_scangle_other 1.908 r_scbond_it 1.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.473 r_dihedral_angle_4_deg 18.055 r_dihedral_angle_3_deg 12.84 r_long_range_B_refined 6.491 r_dihedral_angle_1_deg 6.349 r_long_range_B_other 6.304 r_angle_other_deg 2.073 r_angle_refined_deg 2.011 r_scangle_other 1.908 r_scbond_it 1.235 r_scbond_other 1.224 r_mcangle_it 1.138 r_mcangle_other 1.138 r_mcbond_it 0.693 r_mcbond_other 0.692 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_bond_other_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.01 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 9310 Nucleic Acid Atoms Solvent Atoms 1004 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing