5U9K

Crystal structure of V71F mutant 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 5U9A 

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
2.3146.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.79α = 90
b = 65.07β = 90
c = 106.18γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSRDI CMOS_8M2016-11-09MSINGLE 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
12.740.52299.90.064123.312.4519567.67
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)
12.72.8599.70.7870.9663.211.6

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 REPLACEMENTTHROUGHOUT5U9A2.740.52492625099.880.203340.200690.25741RANDOM83.991
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]
8.290.48-8.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.862
r_dihedral_angle_3_deg18.065
r_long_range_B_refined13.499
r_long_range_B_other13.494
r_dihedral_angle_4_deg11.288
r_scangle_other9.913
r_mcangle_it9.142
r_mcangle_other9.137
r_dihedral_angle_1_deg8.248
r_scbond_it6.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.862
r_dihedral_angle_3_deg18.065
r_long_range_B_refined13.499
r_long_range_B_other13.494
r_dihedral_angle_4_deg11.288
r_scangle_other9.913
r_mcangle_it9.142
r_mcangle_other9.137
r_dihedral_angle_1_deg8.248
r_scbond_it6.195
r_scbond_other6.193
r_mcbond_other5.82
r_mcbond_it5.817
r_angle_refined_deg1.598
r_angle_other_deg0.964
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 Atoms1246
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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