☰ Navigation Tabs
Crystal structure of AtFKBP53 FKBD in complex with rapamycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.2 M Lithium sulfate monohydrate, 0.1 M Bis-Tris (pH 6.5), 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.301 α = 90 b = 73.949 β = 101.01 c = 61.95 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 PIXEL DECTRIS EIGER X 4M 2017-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9677 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 47.01 99.2 0.063 0.998 11 4.4 32798 19.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.65 98.6 0.541 0.743 2.3 4.3
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 6J2M 1.6 47.01 31104 1666 99.1 0.17814 0.17662 0.2102 0.20668 0.2386 RANDOM 18.01
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] -0.04 0.08 0.48 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.135 r_dihedral_angle_4_deg 15.549 r_long_range_B_other 15.432 r_long_range_B_refined 15.416 r_scangle_other 14.844 r_scbond_it 12.267 r_scbond_other 12.262 r_dihedral_angle_3_deg 11.396 r_dihedral_angle_1_deg 6.697 r_mcangle_other 3.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.135 r_dihedral_angle_4_deg 15.549 r_long_range_B_other 15.432 r_long_range_B_refined 15.416 r_scangle_other 14.844 r_scbond_it 12.267 r_scbond_other 12.262 r_dihedral_angle_3_deg 11.396 r_dihedral_angle_1_deg 6.697 r_mcangle_other 3.819 r_mcangle_it 3.816 r_mcbond_it 3.39 r_mcbond_other 3.39 r_angle_refined_deg 1.417 r_angle_other_deg 1.008 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1778 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing