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Crystal structure of human ribokinase in P212121 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 8.5 277 0.1M Tris, 8% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.25 α = 90 b = 65.48 β = 90 c = 180.56 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 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 1.75 47.74 99.5 0.086 16.2 10.6 67798 22.15
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 1.75 1.8 98.7 0.962 2.3 10.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FV7 1.75 47.74 64402 3322 99.44 0.19221 0.19034 0.2009 0.22882 0.238 RANDOM 34.057
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] -0.76 1.36 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.313 r_dihedral_angle_4_deg 17.275 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_1_deg 6.51 r_long_range_B_refined 5.747 r_long_range_B_other 5.642 r_scangle_other 2.994 r_angle_refined_deg 2.275 r_mcangle_it 2.086 r_mcangle_other 2.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.313 r_dihedral_angle_4_deg 17.275 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_1_deg 6.51 r_long_range_B_refined 5.747 r_long_range_B_other 5.642 r_scangle_other 2.994 r_angle_refined_deg 2.275 r_mcangle_it 2.086 r_mcangle_other 2.086 r_scbond_it 1.969 r_scbond_other 1.969 r_angle_other_deg 1.834 r_mcbond_it 1.413 r_mcbond_other 1.413 r_chiral_restr 0.136 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 r_bond_other_d 0.011 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 4591 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing