9GQB | pdb_00009gqb

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog p5(2,1)-Diol-II

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TW7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	24% PEG3350, 0.2M ammonium thiocyanate, 0.1M HEPES-NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.191	α = 90
b = 48.191	β = 90
c = 191.561	γ = 120

Symmetry
Space Group	P 32 2 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 PILATUS3 S 6M		2022-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918400	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	47.89	100	0.048	0.053	0.022	0.999	24	10.4		18383

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.05	100		0.527	0.579	0.238	0.918	4.6	11.2

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-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	41.769	18324	867	99.935	0.221	0.2187	0.219	0.2709	0.27	49.966

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]
-0.547	-0.273		-0.547		1.774

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.037
r_dihedral_angle_6_deg	16.963
r_dihedral_angle_3_deg	13.325
r_dihedral_angle_1_deg	8.337
r_lrange_it	7.281
r_lrange_other	7.279
r_scangle_it	5.439
r_scangle_other	5.437
r_mcangle_it	4.479
r_mcangle_other	4.478
r_scbond_it	4.153
r_scbond_other	4.151
r_mcbond_it	3.56
r_mcbond_other	3.54
r_angle_refined_deg	2.43
r_angle_other_deg	0.797
r_symmetry_xyhbond_nbd_refined	0.308
r_nbd_refined	0.214
r_symmetry_xyhbond_nbd_other	0.212
r_symmetry_nbd_other	0.211
r_nbd_other	0.192
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.176
r_symmetry_nbd_refined	0.168
r_ncsr_local_group_1	0.122
r_chiral_restr	0.121
r_symmetry_nbtor_other	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1851
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
autoXDS	data reduction
Aimless	data scaling
PHASER	phasing