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Crystal structure of human ribokinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RKS pdb entries 1RKS, 1VM7 experimental model PDB 1VM7 pdb entries 1RKS, 1VM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 40% PEG-550MME, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.53 α = 90 b = 72.978 β = 91.08 c = 90.958 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 2005-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
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 2.1 50 99.3 0.046 13.6 3 34881
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 2.1 2.18 97.8 0.261 3
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 (All) 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 pdb entries 1RKS, 1VM7 2.1 30 34605 1770 99.186 0.201 0.201 0.1979 0.2344 0.2484 0.2818 thin shells 23.979
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] -0.083 -0.018 0.062 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.534 r_dihedral_angle_4_deg 16.233 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 4.528 r_scangle_it 2.561 r_scbond_it 1.537 r_angle_refined_deg 1.462 r_scangle_other 1.286 r_mcangle_it 0.926 r_angle_other_deg 0.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.534 r_dihedral_angle_4_deg 16.233 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 4.528 r_scangle_it 2.561 r_scbond_it 1.537 r_angle_refined_deg 1.462 r_scangle_other 1.286 r_mcangle_it 0.926 r_angle_other_deg 0.914 r_mcbond_it 0.493 r_mcangle_other 0.424 r_scbond_other 0.325 r_symmetry_vdw_other 0.223 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.192 r_nbd_other 0.183 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.11 r_mcbond_other 0.104 r_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.017 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4524 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction