5U9A

Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LAV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291100 mM Na-Citrate 20% (W/V) PEG 4000 20 % (V/V) 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
2.3748.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.1α = 90
b = 65.74β = 90
c = 107.04γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSRDI CMOS_8M2016-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.753.521000.077124.913.8533156.92
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)RedundancyNumber Unique Reflections (All)
12.72.8599.90.6920.9824.413

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4LAV2.753.52502628699.940.215670.211620.28932RANDOM76.114
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]
5.224.22-9.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.885
r_dihedral_angle_3_deg17.034
r_dihedral_angle_4_deg11.743
r_long_range_B_refined10.778
r_long_range_B_other10.776
r_dihedral_angle_1_deg7.456
r_scangle_other7.364
r_mcangle_it7.333
r_mcangle_other7.329
r_mcbond_other4.688
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.885
r_dihedral_angle_3_deg17.034
r_dihedral_angle_4_deg11.743
r_long_range_B_refined10.778
r_long_range_B_other10.776
r_dihedral_angle_1_deg7.456
r_scangle_other7.364
r_mcangle_it7.333
r_mcangle_other7.329
r_mcbond_other4.688
r_mcbond_it4.687
r_scbond_it4.448
r_scbond_other4.443
r_angle_refined_deg1.463
r_angle_other_deg0.95
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms1230
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
XDSdata scaling
MoRDaphasing
Cootmodel building
SCALAdata scaling
XDSdata reduction