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Crystal structure of human ribokinase in C2 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% isopropanol, 20% PEG 4000, 0.1M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.41 49.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.92 α = 90 b = 47.04 β = 98.73 c = 80.91 γ = 90
Symmetry Space Group C 1 2 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 315r 2008-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
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 45.49 99.8 0.132 11.5 5.6 49417 13.799
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 98.7 1.002 1.9 5.5
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 45.49 46908 2508 99.81 0.17507 0.17263 0.1827 0.22044 0.2265 RANDOM 28.526
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] -0.71 -0.49 1.01 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.162 r_dihedral_angle_4_deg 20.056 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 6.476 r_long_range_B_refined 5.867 r_long_range_B_other 5.684 r_scangle_other 2.17 r_angle_refined_deg 2.112 r_angle_other_deg 1.641 r_mcangle_it 1.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.162 r_dihedral_angle_4_deg 20.056 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 6.476 r_long_range_B_refined 5.867 r_long_range_B_other 5.684 r_scangle_other 2.17 r_angle_refined_deg 2.112 r_angle_other_deg 1.641 r_mcangle_it 1.404 r_mcangle_other 1.404 r_scbond_it 1.352 r_scbond_other 1.352 r_mcbond_it 0.907 r_mcbond_other 0.906 r_chiral_restr 0.126 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.01 r_gen_planes_other 0.008 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 4700 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing