5V35

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U9A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION291100 mM Na-Citrate 20 % (W/V) PEG 4000 20 % (V/V) 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
2.448.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.15α = 90
b = 65.52β = 90
c = 106.95γ = 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
12.553.47599.80.0550.99923.813.8674463.99
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)RedundancyNumber Unique Reflections (All)
12.52.6499.90.6810.9843.513741

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 REPLACEMENTTHROUGHOUT5U9A2.553.47639333199.820.218710.216010.27242RANDOM76.432
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]
7.791.19-8.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.885
r_dihedral_angle_3_deg18.039
r_dihedral_angle_4_deg12.946
r_long_range_B_refined12.66
r_long_range_B_other12.656
r_scangle_other9.439
r_mcangle_it9.237
r_mcangle_other9.231
r_dihedral_angle_1_deg6.756
r_mcbond_other6.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.885
r_dihedral_angle_3_deg18.039
r_dihedral_angle_4_deg12.946
r_long_range_B_refined12.66
r_long_range_B_other12.656
r_scangle_other9.439
r_mcangle_it9.237
r_mcangle_other9.231
r_dihedral_angle_1_deg6.756
r_mcbond_other6.371
r_mcbond_it6.369
r_scbond_it6.303
r_scbond_other6.301
r_angle_refined_deg1.729
r_angle_other_deg1.011
r_chiral_restr0.095
r_bond_refined_d0.014
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 Atoms1174
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms15

Software

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