4DRI | pdb_00004dri

Co-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of mTOR

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	25% PEG3350, 0.1 M NaCl, 0.1M HEPES-NaOH pH 7.5, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.503	α = 90
b = 59.554	β = 90
c = 67.787	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 315r		2008-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9788	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.45	67.787	95.7	0.043	0.043	17.3	3.8	41315	41315			18.77

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	93.8		0.377	0.377	2	3.5	5806

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 1FAP	1.45	19.05	41275	39213	2062	95.16	0.1784	0.1784	0.1769	0.17	0.2064	0.21	RANDOM	25.4582

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]
-0.04			-0.04		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.618
r_dihedral_angle_4_deg	16.59
r_dihedral_angle_3_deg	13.009
r_dihedral_angle_1_deg	6.778
r_scangle_it	3.471
r_scbond_it	2.281
r_angle_refined_deg	1.546
r_mcangle_it	1.435
r_mcbond_it	0.954
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.618
r_dihedral_angle_4_deg	16.59
r_dihedral_angle_3_deg	13.009
r_dihedral_angle_1_deg	6.778
r_scangle_it	3.471
r_scbond_it	2.281
r_angle_refined_deg	1.546
r_mcangle_it	1.435
r_mcbond_it	0.954
r_nbtor_refined	0.312
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.1
r_symmetry_hbond_refined	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1718
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	65

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.