9PJ1 | pdb_00009pj1

Crystal structure of a synthetic Fab (4R) in complex with the ternary assembly of FKBP12, Rapamycin, and the FRB domain of mTOR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MDJ
experimental model	PDB	1FAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.15 M Ammonium sulfate, 0.1 M TRIS pH 8.0, 17.5% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.72	α = 90
b = 72.86	β = 103.05
c = 85.9	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	61.18	98.14	0.993	4.96	1.9		46596

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09			0.363	1.33

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.05	61.18	46587	2286	98.16	0.1985	0.2057	0.2287	0.2349	24.41

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]
-0.94		-0.56	1.5		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.619
r_dihedral_angle_3_deg	11.65
r_dihedral_angle_1_deg	6.368
r_scangle_it	5.227
r_scangle_other	5.227
r_mcangle_it	4.126
r_mcangle_other	4.126
r_scbond_it	3.352
r_scbond_other	3.351
r_mcbond_it	2.586
r_mcbond_other	2.581
r_angle_refined_deg	0.874
r_angle_other_deg	0.318
r_nbd_refined	0.176
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.134
r_nbd_other	0.131
r_chiral_restr	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbtor_other
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_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4900
Nucleic Acid Atoms
Solvent Atoms	501
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing