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Small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KGP PDB ENTRY 1KGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 27.5% PEG4000, 0.05M Ammonium acetate pH 6.0, 0.1 M ammonium acetate pH 7.0, 0.1 M Sodium citrate, 0.05 M Tris-HCL pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.21 α = 90 b = 87.683 β = 99.29 c = 83.249 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 225 mm CCD 2008-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00000 SPring-8 BL41XU
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 1.36 50 96.1 0.073 9 3.6 140012 1 1
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) 1.36 1.41 72.7 0.477 2.8 10540
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FREE R PDB ENTRY 1KGP 1.36 20 132961 101769 7008 91.2 0.15 0.15 0.1591 0.21 0.2021 RANDOM 17.407
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]
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.057 s_non_zero_chiral_vol 0.053 s_zero_chiral_vol 0.051 s_angle_d 0.026 s_from_restr_planes 0.021 s_anti_bump_dis_restr 0.017 s_bond_d 0.01 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4838 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing SHELX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SHELXL-97 refinement