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Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from Homo sapiens at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 2.0M ammonium sulfate, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.12 60.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.053 α = 90 b = 98.762 β = 90 c = 133.668 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 PIXEL DECTRIS PILATUS 6M Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2011-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 29.834 97.5 0.105 9.8 6.3 45830 45830
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 95.8 0.73 0.73 1.7 3.9 3169
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.2 29.834 45754 2320 97.14 0.1945 0.1931 0.2016 0.2191 0.2247 RANDOM 56.1845
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] 1.07 0.88 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.007 r_dihedral_angle_4_deg 15.375 r_dihedral_angle_3_deg 14.822 r_dihedral_angle_1_deg 4.95 r_angle_refined_deg 1.173 r_angle_other_deg 1.108 r_nbd_refined 0.216 r_nbd_other 0.21 r_symmetry_vdw_refined 0.2 r_symmetry_vdw_other 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.007 r_dihedral_angle_4_deg 15.375 r_dihedral_angle_3_deg 14.822 r_dihedral_angle_1_deg 4.95 r_angle_refined_deg 1.173 r_angle_other_deg 1.108 r_nbd_refined 0.216 r_nbd_other 0.21 r_symmetry_vdw_refined 0.2 r_symmetry_vdw_other 0.188 r_nbtor_refined 0.187 r_nbtor_other 0.104 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4674 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 13
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing SCALA data scaling REFMAC refinement MOSFLM data reduction SHELXD phasing