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Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HNC PDB entry 3HNC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 298 0.1 M Tris-HCl pH 7.9, 0.2 M LiSO4, 19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.147 α = 90 b = 114.372 β = 90 c = 222.474 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 MARMOSAIC 300 mm CCD 2008-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9000 APS 23-ID-B
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 3 50 91.7 0.131 9.755 6.6 32613
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) 3 3.11 93.8 0.657 6
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 PDB entry 3HNC 3.11 44.07 27243 1440 88.49 0.18915 0.18473 0.1881 0.27459 0.2743 RANDOM 65.226
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] 0.81 -1.98 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.422 r_dihedral_angle_3_deg 22.243 r_dihedral_angle_4_deg 18.708 r_dihedral_angle_1_deg 6.844 r_scangle_it 2.149 r_angle_refined_deg 1.672 r_scbond_it 1.294 r_mcangle_it 0.901 r_mcbond_it 0.481 r_metal_ion_refined 0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.422 r_dihedral_angle_3_deg 22.243 r_dihedral_angle_4_deg 18.708 r_dihedral_angle_1_deg 6.844 r_scangle_it 2.149 r_angle_refined_deg 1.672 r_scbond_it 1.294 r_mcangle_it 0.901 r_mcbond_it 0.481 r_metal_ion_refined 0.341 r_nbtor_refined 0.321 r_nbd_refined 0.249 r_symmetry_vdw_refined 0.248 r_symmetry_hbond_refined 0.238 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11205 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 123
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection