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Crystal structure of secreted chorismate mutase from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 Well solution: 1.5-1.6 M ammonium sulfate, 0.1 M citrate/phosphate buffer pH 4.2. Protein solution: 5 mg/ml in 0.025 M Tris ph 7.5, 0.0005 M EDTA, 0.0005 M DTT, 0.1 M sodium chloride. Drops: 1:1 well:protein., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.01 α = 90 b = 144.09 β = 90 c = 116.63 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 ADSC QUANTUM 315 2005-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979 NSLS X29A
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 2.1 50 99.4 0.113 8.2 13 43510
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) 2.1 2.18 95.3 0.469 8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.1 20 42698 2177 97.48 0.21 0.207 0.2124 0.258 0.256 RANDOM 35.383
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] 1.21 -0.13 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.061 r_dihedral_angle_4_deg 22.026 r_dihedral_angle_3_deg 18.479 r_dihedral_angle_1_deg 6.973 r_scangle_it 4.478 r_scbond_it 3.065 r_mcangle_it 1.986 r_angle_refined_deg 1.857 r_mcbond_it 1.25 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.061 r_dihedral_angle_4_deg 22.026 r_dihedral_angle_3_deg 18.479 r_dihedral_angle_1_deg 6.973 r_scangle_it 4.478 r_scbond_it 3.065 r_mcangle_it 1.986 r_angle_refined_deg 1.857 r_mcbond_it 1.25 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.176 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4923 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 117
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction