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Phosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 1 M tri-sodium citrate, 0.1 M sodium cacodylate, 0.01 M coenzyme A, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.21 70.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.82 α = 90 b = 114.82 β = 90 c = 119.074 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 ADSC QUANTUM 315 2009-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.89 38.2 100 0.065 9.5 12.3 24323 24323 40.3
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 1.89 1.92 100 0.836 3.81 12.4 1205
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 1H1T 1.89 38.2 24310 24310 1239 99.97 0.165 0.165 0.164 0.1631 0.192 0.1892 RANDOM 26.902
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] -0.79 -0.4 -0.79 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.323 r_dihedral_angle_4_deg 19.172 r_dihedral_angle_3_deg 16.603 r_dihedral_angle_1_deg 5.055 r_scangle_it 4.478 r_scbond_it 2.952 r_mcangle_it 1.87 r_angle_refined_deg 1.866 r_mcbond_it 1.055 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.323 r_dihedral_angle_4_deg 19.172 r_dihedral_angle_3_deg 16.603 r_dihedral_angle_1_deg 5.055 r_scangle_it 4.478 r_scbond_it 2.952 r_mcangle_it 1.87 r_angle_refined_deg 1.866 r_mcbond_it 1.055 r_chiral_restr 0.123 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1243 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction MOLREP phasing HKL-3000 phasing