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Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and dATP
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 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.856 α = 90 b = 114.388 β = 90 c = 220.003 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 MAR CCD 165 mm 2008-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.9000 APS 14-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 90.4 0.155 9.651 5.3 31793
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 0.644 3.6
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 3.16 40.86 26016 1335 89.39 0.18895 0.18509 0.1855 0.2602 0.2632 RANDOM 63.329
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] 1.5 -3.54 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.031 r_dihedral_angle_3_deg 21.412 r_dihedral_angle_4_deg 17.083 r_dihedral_angle_1_deg 6.549 r_scangle_it 1.703 r_angle_refined_deg 1.458 r_scbond_it 1.024 r_mcangle_it 0.754 r_mcbond_it 0.408 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.031 r_dihedral_angle_3_deg 21.412 r_dihedral_angle_4_deg 17.083 r_dihedral_angle_1_deg 6.549 r_scangle_it 1.703 r_angle_refined_deg 1.458 r_scbond_it 1.024 r_mcangle_it 0.754 r_mcbond_it 0.408 r_nbtor_refined 0.316 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_refined 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 11391 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 110
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection