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Crystal structure of V71F mutant of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with S-farnesyl-L-cysteine methyl ester
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 100 mM Na-Citrate
20 % (W/V) PEG 4000
20 % (V/V) 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.4 48.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.15 α = 90 b = 65.52 β = 90 c = 106.95 γ = 90
Symmetry Space Group C 2 2 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 CMOS RDI CMOS_8M 2016-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1 ALS 4.2.2
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 2.5 53.475 99.8 0.055 0.999 23.8 13.8 6744 63.99
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 2.5 2.64 99.9 0.681 0.984 3.5 13 741
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 5U9A 2.5 53.47 6393 331 99.82 0.21871 0.21601 0.2271 0.27242 0.2734 RANDOM 76.432
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] 7.79 1.19 -8.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_3_deg 18.039 r_dihedral_angle_4_deg 12.946 r_long_range_B_refined 12.66 r_long_range_B_other 12.656 r_scangle_other 9.439 r_mcangle_it 9.237 r_mcangle_other 9.231 r_dihedral_angle_1_deg 6.756 r_mcbond_other 6.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_3_deg 18.039 r_dihedral_angle_4_deg 12.946 r_long_range_B_refined 12.66 r_long_range_B_other 12.656 r_scangle_other 9.439 r_mcangle_it 9.237 r_mcangle_other 9.231 r_dihedral_angle_1_deg 6.756 r_mcbond_other 6.371 r_mcbond_it 6.369 r_scbond_it 6.303 r_scbond_other 6.301 r_angle_refined_deg 1.729 r_angle_other_deg 1.011 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1174 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection XDS data scaling PHASER phasing Coot model building