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Crystal structure of human ribonucleotide reductase 1 bound to the effector TTP and substrate GDP
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 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.159 α = 90 b = 115.834 β = 90 c = 221.305 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 3.1 50 98.7 0.104 12.417 4.8 34010
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) 3.1 3.21 96.2 0.583 4
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 3.21 49.94 29455 1576 98.13 0.18347 0.17966 0.1867 0.25389 0.2514 RANDOM 104.779
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] 1.92 0.1 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.636 r_dihedral_angle_3_deg 21.499 r_dihedral_angle_4_deg 20.46 r_dihedral_angle_1_deg 6.912 r_scangle_it 2.097 r_angle_refined_deg 1.55 r_scbond_it 1.21 r_mcangle_it 0.871 r_mcbond_it 0.474 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.636 r_dihedral_angle_3_deg 21.499 r_dihedral_angle_4_deg 20.46 r_dihedral_angle_1_deg 6.912 r_scangle_it 2.097 r_angle_refined_deg 1.55 r_scbond_it 1.21 r_mcangle_it 0.871 r_mcbond_it 0.474 r_nbtor_refined 0.319 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.244 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.102 r_metal_ion_refined 0.065 r_bond_refined_d 0.014 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 11397 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 136
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection PHASER phasing