5V35 | pdb_00005v35

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

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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	0.23	0.27242	0.27	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
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