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Human Ribonucleotide reductase R1 subunit (RRM1) in complex with dATP and Mg.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYZ PDB ENTRY 1ZYZ
Crystallization Crystal Properties Matthews coefficient Solvent content 2.21 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.95 α = 90 b = 129.31 β = 95.5 c = 76.67 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 CCD 2009-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.3 49 98.4 0.1 10.7 3.8 56722
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 2.3 2.4 97.7 0.45 3 3.8
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 1ZYZ 2.3 48.85 53884 2837 100 0.1955 0.19222 0.1977 0.25762 0.2622 RANDOM 21.629
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] 1.36 3.99 -2.92 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.283 r_dihedral_angle_4_deg 19.263 r_dihedral_angle_3_deg 17.692 r_dihedral_angle_1_deg 6.722 r_scangle_it 3.407 r_scbond_it 2.147 r_angle_refined_deg 1.613 r_mcangle_it 1.367 r_angle_other_deg 0.952 r_mcbond_it 0.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.283 r_dihedral_angle_4_deg 19.263 r_dihedral_angle_3_deg 17.692 r_dihedral_angle_1_deg 6.722 r_scangle_it 3.407 r_scbond_it 2.147 r_angle_refined_deg 1.613 r_mcangle_it 1.367 r_angle_other_deg 0.952 r_mcbond_it 0.738 r_mcbond_other 0.161 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10357 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling