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Crystal structure of peptidyl-prolyl cis-trans isomerase from Encephalitozoon cuniculi at 1.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIU PDB entry 2BIU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 HAMPTON RESEARCH CRYSTAL SCREEN CONDITION B5: 200mM Li sulfate, 100mM Tris-HCl pH 8.5, 30% PEG 4000; Protein at 49.8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K
Crystal Properties Matthews coefficient Solvent content 2.09 41.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.81 α = 90.01 b = 73.86 β = 79.1 c = 63.59 γ = 90.02
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 2009-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97351 CLSI 08ID-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 1.95 40 94.4 0.052 11.91 2 50563 47719 -3 26.23
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) 1.95 2 94.7 0.276 3 2 50563
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2BIU 1.95 40 47718 47718 2442 94.4 0.166 0.166 0.163 0.1707 0.216 0.2194 RANDOM 17.33
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] -0.55 -0.11 1.3 1.21 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.294 r_dihedral_angle_4_deg 18.306 r_dihedral_angle_3_deg 12.428 r_dihedral_angle_1_deg 6.754 r_scangle_it 4.221 r_scbond_it 2.571 r_mcangle_it 1.583 r_angle_refined_deg 1.515 r_mcbond_it 0.913 r_angle_other_deg 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.294 r_dihedral_angle_4_deg 18.306 r_dihedral_angle_3_deg 12.428 r_dihedral_angle_1_deg 6.754 r_scangle_it 4.221 r_scbond_it 2.571 r_mcangle_it 1.583 r_angle_refined_deg 1.515 r_mcbond_it 0.913 r_angle_other_deg 0.895 r_mcbond_other 0.251 r_chiral_restr 0.096 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5298 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 42
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling