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Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 100 mM Na-Citrate
20% (W/V) PEG 4000
20 % (V/V) 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.1 α = 90 b = 65.74 β = 90 c = 107.04 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 2016-09-22 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 2.7 53.52 100 0.077 1 24.9 13.8 5331 56.92
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 2.7 2.85 99.9 0.692 0.982 4.4 13
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 4LAV 2.7 53.52 5026 286 99.94 0.21567 0.21162 0.2196 0.28932 0.2933 RANDOM 76.114
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] 5.22 4.22 -9.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.885 r_dihedral_angle_3_deg 17.034 r_dihedral_angle_4_deg 11.743 r_long_range_B_refined 10.778 r_long_range_B_other 10.776 r_dihedral_angle_1_deg 7.456 r_scangle_other 7.364 r_mcangle_it 7.333 r_mcangle_other 7.329 r_mcbond_other 4.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.885 r_dihedral_angle_3_deg 17.034 r_dihedral_angle_4_deg 11.743 r_long_range_B_refined 10.778 r_long_range_B_other 10.776 r_dihedral_angle_1_deg 7.456 r_scangle_other 7.364 r_mcangle_it 7.333 r_mcangle_other 7.329 r_mcbond_other 4.688 r_mcbond_it 4.687 r_scbond_it 4.448 r_scbond_other 4.443 r_angle_refined_deg 1.463 r_angle_other_deg 0.95 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 1230 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection XDS data scaling MoRDa phasing Coot model building SCALA data scaling XDS data reduction