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Crystal structure of a Peptidyl-prolyl cis-trans isomerase with surface mutation R92G from Burkholderia pseudomallei complexed with FK506
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VAW PDB entry 3vaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Internal tracking number 224744. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D239 PD00214 21.8mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 3.09 60.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.44 α = 90 b = 49.05 β = 123.05 c = 66.64 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+ 2011-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2 44.61 97.5 0.047 26.88 6.44 19744 19250 -3 -3 23.506
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 2.05 96.6 0.131 9.1
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 MR THROUGHOUT PDB entry 3vaw 2 44.61 19744 18755 950 95.29 0.22 0.22 0.219 0.2212 0.247 0.2287 RANDOM 21.826
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] -0.94 -0.35 1.09 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.937 r_dihedral_angle_4_deg 21.543 r_dihedral_angle_3_deg 11.77 r_dihedral_angle_1_deg 6.664 r_angle_refined_deg 1.473 r_angle_other_deg 0.89 r_chiral_restr 0.071 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.937 r_dihedral_angle_4_deg 21.543 r_dihedral_angle_3_deg 11.77 r_dihedral_angle_1_deg 6.664 r_angle_refined_deg 1.473 r_angle_other_deg 0.89 r_chiral_restr 0.071 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1650 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 116
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction