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Crystal structure of a Peptidyl-prolyl cis-trans isomerase with surface mutation M61H 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 226597. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D227 PD00193 25.2mg/ml., vapor diffusion, sitting drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.94 58.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.98 α = 90 b = 106.58 β = 90 c = 107.16 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 225 mm CCD mirrors 2012-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978720 APS 21-ID-F
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 47.72 99.9 0.09 14.17 4.87 19417 19388 -3 -3 26.545
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 2.05 100 0.503 3.3
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 47.72 19417 19360 991 99.86 0.193 0.193 0.192 0.2045 0.219 0.2281 RANDOM 22.101
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] -0.31 -1.21 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.514 r_dihedral_angle_4_deg 12.401 r_dihedral_angle_3_deg 10.932 r_dihedral_angle_1_deg 5.886 r_angle_refined_deg 1.518 r_angle_other_deg 0.993 r_chiral_restr 0.064 r_bond_refined_d 0.015 r_bond_other_d 0.004 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.514 r_dihedral_angle_4_deg 12.401 r_dihedral_angle_3_deg 10.932 r_dihedral_angle_1_deg 5.886 r_angle_refined_deg 1.518 r_angle_other_deg 0.993 r_chiral_restr 0.064 r_bond_refined_d 0.015 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 160
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction