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Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup
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 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.79 α = 90 b = 72.42 β = 90.43 c = 92.75 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 315 2009-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9789 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 1.5 27.12 99.2 0.062 11.7 3.7 96118 12.297
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 1.5 1.54 98.4 0.643 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 1.5 27.12 91278 4826 99.16 0.12931 0.12659 0.1257 0.18132 0.1809 RANDOM 20.356
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] 0.4 0.12 -0.25 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.777 r_sphericity_free 27.063 r_dihedral_angle_4_deg 17.527 r_dihedral_angle_3_deg 11.931 r_sphericity_bonded 10.744 r_rigid_bond_restr 6.618 r_dihedral_angle_1_deg 6.002 r_long_range_B_refined 4.442 r_scangle_other 4.18 r_scbond_it 3.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.777 r_sphericity_free 27.063 r_dihedral_angle_4_deg 17.527 r_dihedral_angle_3_deg 11.931 r_sphericity_bonded 10.744 r_rigid_bond_restr 6.618 r_dihedral_angle_1_deg 6.002 r_long_range_B_refined 4.442 r_scangle_other 4.18 r_scbond_it 3.965 r_long_range_B_other 3.943 r_scbond_other 3.938 r_mcangle_other 2.904 r_mcangle_it 2.894 r_mcbond_other 2.564 r_mcbond_it 2.557 r_angle_refined_deg 2.324 r_angle_other_deg 1.856 r_chiral_restr 0.154 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_bond_other_d 0.012 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4620 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing