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Crystal structure of Pichia pastoris Pex8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.09M NPS, 0.1M pH 7.5 (Sodium HEPES + MOPS), 12% Ethylene glycol, 6% w/v PEG 8000, 4% Formamide
Crystal Properties Matthews coefficient Solvent content 3.36 63.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.149 α = 90 b = 87.842 β = 90 c = 153.093 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER2 X 16M 2019-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.41 47.03 100 0.188 0.204 0.077 0.999 10 13.2 43103 60.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.5 4.834 5.212 1.943 0.415 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.41 47.03 43038 2088 99.972 0.214 0.2122 0.2106 0.2581 0.257 76.887
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] -1.62 1.762 -0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.376 r_dihedral_angle_3_deg 15.213 r_lrange_it 8.053 r_lrange_other 8.052 r_dihedral_angle_2_deg 6.869 r_dihedral_angle_1_deg 6.3 r_scangle_it 6.213 r_scangle_other 6.212 r_mcangle_it 5.29 r_mcangle_other 5.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.376 r_dihedral_angle_3_deg 15.213 r_lrange_it 8.053 r_lrange_other 8.052 r_dihedral_angle_2_deg 6.869 r_dihedral_angle_1_deg 6.3 r_scangle_it 6.213 r_scangle_other 6.212 r_mcangle_it 5.29 r_mcangle_other 5.289 r_scbond_it 3.971 r_scbond_other 3.97 r_mcbond_it 3.417 r_mcbond_other 3.417 r_angle_refined_deg 1.582 r_angle_other_deg 0.572 r_symmetry_xyhbond_nbd_refined 0.515 r_nbd_refined 0.234 r_nbd_other 0.194 r_nbtor_refined 0.193 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.139 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.072 r_symmetry_xyhbond_nbd_other 0.011 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5016 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction Coot model building AutoSol phasing PHASER phasing