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Crystal structure of Proline iminopeptidase Mycobacterium smegmatis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG 3350, 0.2 M sodium citrate, 0.1 M Tris propane, pH 8.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.93 α = 90 b = 69.92 β = 93.18 c = 55.63 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 RIGAKU SATURN 944+ 2010-05-14 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.8 50 94.8 0.117 12.87 24228 -3 17.989
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 1.8 1.85 55.8 0.527 2.2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 37.94 21658 1104 99.49 0.138 0.136 0.173 0.1468 RANDOM 10.295
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] 0.23 0.17 -0.17 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.803 r_dihedral_angle_4_deg 20.089 r_dihedral_angle_3_deg 12.861 r_dihedral_angle_1_deg 5.757 r_scangle_it 2.93 r_scbond_it 1.904 r_angle_refined_deg 1.412 r_mcangle_it 1.112 r_angle_other_deg 0.957 r_mcbond_it 0.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.803 r_dihedral_angle_4_deg 20.089 r_dihedral_angle_3_deg 12.861 r_dihedral_angle_1_deg 5.757 r_scangle_it 2.93 r_scbond_it 1.904 r_angle_refined_deg 1.412 r_mcangle_it 1.112 r_angle_other_deg 0.957 r_mcbond_it 0.668 r_mcbond_other 0.208 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2304 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 17
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction