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Apo Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase I87T mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H9D PDB ENTRY 2H9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298.15 0.1M Bis-tris propane, pH 6.5, 0.14 M calcium chloride, 23% PEG 3350, and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
Crystal Properties Matthews coefficient Solvent content 2.01 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.503 α = 90 b = 74.919 β = 90 c = 88.505 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113.15 IMAGE PLATE RIGAKU RAXIS IV++ 2006-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54
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 2.25 100 99.3 0.1 14.686 7 17729
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) 2.25 2.33 98.5 0.354 7 1726
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2H9D 2.25 23.21 17678 900 99.31 0.221 0.219 0.256 0.26 RANDOM 20.028
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] 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.775 r_dihedral_angle_4_deg 14.815 r_dihedral_angle_3_deg 14.049 r_dihedral_angle_1_deg 4.682 r_scangle_it 2.137 r_scbond_it 1.296 r_angle_refined_deg 1.023 r_mcangle_it 0.824 r_mcbond_it 0.555 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.775 r_dihedral_angle_4_deg 14.815 r_dihedral_angle_3_deg 14.049 r_dihedral_angle_1_deg 4.682 r_scangle_it 2.137 r_scbond_it 1.296 r_angle_refined_deg 1.023 r_mcangle_it 0.824 r_mcbond_it 0.555 r_nbtor_refined 0.292 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.074 r_symmetry_metal_ion_refined 0.064 r_metal_ion_refined 0.048 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2722 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing