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X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2 M magnesium acetate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.455 α = 90 b = 53.455 β = 90 c = 220.747 γ = 120
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 RAYONIX MX-300 2015-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.92 50 99 0.086 0.095 0.04 8.8 5 53468
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 88.1 0.814 0.927 0.429 0.547 3.7
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 MOLECULAR REPLACEMENT THROUGHOUT 1.92 50 44358 2367 86.6 0.2077 0.2057 0.2116 0.2456 0.249 RANDOM 24.173
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] 0.07 0.03 0.07 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.013 r_dihedral_angle_4_deg 20.291 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_1_deg 5.486 r_angle_refined_deg 1.246 r_angle_other_deg 0.818 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.013 r_dihedral_angle_4_deg 20.291 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_1_deg 5.486 r_angle_refined_deg 1.246 r_angle_other_deg 0.818 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5059 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing