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Crystal Structure of a Single-Domain Cyclophilin from Brassica napus Phloem Sap
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 The protein concentration was adjusted to 10 mg/ml. The protein solution was supplemented with cyclosporin A at a molar ratio of 2:1 and mixed with the reservoir solution containing 2.4 M sodium malonate, pH 7.0.
Crystal Properties Matthews coefficient Solvent content 3.07 59.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.58 α = 90 b = 86.58 β = 90 c = 119.52 γ = 90
Symmetry Space Group I 41 2 2
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 EIGER X 16M 2017-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 1.0332 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.977 70.12 99.8 0.101 0.112 0.046 9.2 5.6 16197
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.08 100 0.466 0.466 0.513 0.21 1.6 5.9
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 4jjm 1.98 70.12 15368 813 99.92 0.1856 0.1838 0.1976 0.2231 0.2348 RANDOM 33.262
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] 1.68 1.68 -3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.626 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_4_deg 13.449 r_dihedral_angle_1_deg 6.389 r_angle_refined_deg 2.011 r_angle_other_deg 1.157 r_chiral_restr 0.154 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.626 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_4_deg 13.449 r_dihedral_angle_1_deg 6.389 r_angle_refined_deg 2.011 r_angle_other_deg 1.157 r_chiral_restr 0.154 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1279 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 93
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction