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X-ray structure of peptidyl-prolyl cis-trans isomerase A, PpiA, Rv0009, from Mycobacterium tuberculosis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AWR PDB ENTRY 1AWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PROTEIN WAS CO-CRYSTALLIZED WITH THE PEPTIDE HAGPIA (FINAL CONCENTRATION 1 MM) FROM 30% PEG-200, 5% PEG-3000, 0.1 M MES-HCL PH 6.0; THEN SOAKED IN THE RESERVOIR SOLUTION PLUS 1 MM HAGPIA.
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.349 α = 90 b = 65.349 β = 90 c = 102.493 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 110 CCD ADSC CCD SAGITALLY FOCUSING GE(220) AND A MULTILAYER 2004-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.6 32.62 99.6 0.1 6.2 5.4 14896
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 2.6 2.74 99.8 0.59 1.3 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AWR 2.6 30 14230 756 99.7 0.213 0.212 0.2212 0.229 0.2373 RANDOM 61.82
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] 5.21 2.6 5.21 -7.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.826 r_scangle_it 3.268 r_scbond_it 1.779 r_angle_refined_deg 1.404 r_mcangle_it 1.377 r_angle_other_deg 1.011 r_mcbond_it 0.71 r_symmetry_vdw_other 0.395 r_symmetry_vdw_refined 0.265 r_nbd_other 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.826 r_scangle_it 3.268 r_scbond_it 1.779 r_angle_refined_deg 1.404 r_mcangle_it 1.377 r_angle_other_deg 1.011 r_mcbond_it 0.71 r_symmetry_vdw_other 0.395 r_symmetry_vdw_refined 0.265 r_nbd_other 0.25 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.185 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_other 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing