4DRO | pdb_00004dro

EVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND FKBP52: COMPLEX OF FKBP51 WITH (1R)-3-(3,4-dimethoxyphenyl)-1-phenylpropyl (2S)-1-{[(1R,2S)-2-ethyl-1-hydroxycyclohexyl](oxo)acetyl}piperidine-2-carboxylate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	37.5 % PEG3350, 0.1 M NH4OAc, 0.1 M HEPES pH 7.5, 10 % DMSO, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.19	α = 90
b = 54.785	β = 90
c = 56.735	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 210		2010-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.933	ESRF	ID14-1

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	1.099	33.427	99.7	0.067	0.067	10.3	3.5	54139	54139			6.06

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	1.1	1.16	98.7		0.353	0.353	2.2	3.4	7710

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	isomorphous apo crystals	THROUGHOUT	3O5Q	1.1	20	51517	51373	2699	99.72	0.1489	0.1489	0.1477	0.16	0.1725	0.18	RANDOM	9.4608

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			0.03		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.331
r_dihedral_angle_3_deg	11.947
r_dihedral_angle_4_deg	11.313
r_dihedral_angle_1_deg	7.3
r_sphericity_free	6.421
r_scangle_it	3.633
r_sphericity_bonded	2.856
r_scbond_it	2.784
r_mcangle_it	1.976
r_mcbond_it	1.62
r_angle_refined_deg	1.613
r_rigid_bond_restr	1.291
r_angle_other_deg	0.893
r_mcbond_other	0.563
r_symmetry_hbond_refined	0.201
r_nbd_other	0.198
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_other	0.198
r_nbd_refined	0.19
r_nbtor_refined	0.176
r_chiral_restr	0.102
r_symmetry_vdw_refined	0.096
r_nbtor_other	0.095
r_bond_refined_d	0.013
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	986
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	41

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling