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2.05 Angstrom structure of a divalent-cation tolerance protein (CutA) from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NUH PDB entry 2NUH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Protein solution: 0.3M NaCl, 10mM HEPES pH 7.5. Well solution: 20% PEG 3350, 0.2M Sodium citrate, 0.1M HEPES pH 7.5. Cryo solution: 7% Glycerol, 7% Sucrose, 7% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.782 α = 90 b = 157.914 β = 90 c = 157.132 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD beryllium lenses 2009-02-27 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 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 2.05 29.59 98.1 0.094 17.7 5.9 107769 107769 -3 25.4
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 2.05 2.09 94.8 0.506 3.3 5 5167
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 (All) 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 2NUH 2.05 29.59 101920 101920 5358 98.12 0.15868 0.15868 0.15648 0.1533 0.20039 0.1963 RANDOM 26.164
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] -0.34 -0.64 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.891 r_dihedral_angle_4_deg 10.964 r_dihedral_angle_3_deg 9.493 r_scangle_it 5.079 r_scbond_it 3.361 r_dihedral_angle_1_deg 2.777 r_mcangle_it 2.002 r_angle_refined_deg 1.209 r_mcbond_it 1.191 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.891 r_dihedral_angle_4_deg 10.964 r_dihedral_angle_3_deg 9.493 r_scangle_it 5.079 r_scbond_it 3.361 r_dihedral_angle_1_deg 2.777 r_mcangle_it 2.002 r_angle_refined_deg 1.209 r_mcbond_it 1.191 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9936 Nucleic Acid Atoms Solvent Atoms 1187 Heterogen Atoms 313
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling