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Crystal structure of MBP fused split FKBP in complex with rapamycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Na-HEPES buffer (pH 7.5), 20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.026 α = 90 b = 48.144 β = 106.52 c = 108.73 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225-HS 2019-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.92 48.14 100 0.995 7.4 3.8 23633
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.92 3.1 0.79
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FAP 2.92 48.14 22328 1295 99.96 0.21298 0.20806 0.29762 0.2692 RANDOM 52.568
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] 0.61 1.46 -3.27 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.452 r_dihedral_angle_3_deg 14.937 r_dihedral_angle_4_deg 14.037 r_dihedral_angle_1_deg 6.073 r_long_range_B_refined 4.264 r_long_range_B_other 4.263 r_scangle_other 2.904 r_mcangle_it 2.74 r_mcangle_other 2.739 r_scbond_it 2.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.452 r_dihedral_angle_3_deg 14.937 r_dihedral_angle_4_deg 14.037 r_dihedral_angle_1_deg 6.073 r_long_range_B_refined 4.264 r_long_range_B_other 4.263 r_scangle_other 2.904 r_mcangle_it 2.74 r_mcangle_other 2.739 r_scbond_it 2.068 r_scbond_other 2.068 r_rigid_bond_restr 1.994 r_mcbond_it 1.854 r_mcbond_other 1.854 r_angle_refined_deg 1.39 r_angle_other_deg 1.159 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7181 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 136
Software Software Software Name Purpose XDS data reduction MOLREP phasing REFMAC refinement Aimless data scaling