☰ Navigation Tabs
The structure of a Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NUL PDB ENTRY 2NUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 289 50% PEG 400, 0.1M NaAcetate pH 4.5, 200mM Lithium sulfate. Direct cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.23 44.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.657 α = 90 b = 80.657 β = 90 c = 43.338 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 RIGAKU SATURN 944+ VariMax Cu-HF 2011-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.65 50 98.6 0.112 23.8 4 19225
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 1.65 1.68 94.3 0.174 2.3 924
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 2NUL 1.651 23.28 19200 978 98.52 0.1485 0.1467 0.1601 0.1827 0.1927 RANDOM 16.5407
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] -0.11 -0.05 -0.11 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.823 r_dihedral_angle_4_deg 27.253 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 5.74 r_scangle_it 3.93 r_scbond_it 2.284 r_mcangle_it 1.387 r_angle_refined_deg 1.375 r_angle_other_deg 0.904 r_mcbond_it 0.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.823 r_dihedral_angle_4_deg 27.253 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 5.74 r_scangle_it 3.93 r_scbond_it 2.284 r_mcangle_it 1.387 r_angle_refined_deg 1.375 r_angle_other_deg 0.904 r_mcbond_it 0.759 r_mcbond_other 0.217 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1244 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction