9GQ6 | pdb_00009gq6

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog p5(1,2)-H2

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	20% PEG3350, 0.2M ammonium thiocyanate, 0.1M HEPES-NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.843	α = 90
b = 48.843	β = 90
c = 194.255	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	1.88	48.56	99.9	0.043	0.048	0.02	0.999	22	10.6		22952

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)
	1.88	1.92	98.3		1.362	1.516	0.655	0.637	1.6	9.8

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	1.88	42.335	22884	1139	99.856	0.241	0.2393	0.24	0.2737	0.2721	57.493

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]
-0.097	-0.049		-0.097		0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.755
r_dihedral_angle_3_deg	12.931
r_dihedral_angle_1_deg	8.124
r_lrange_other	6.259
r_lrange_it	6.256
r_dihedral_angle_2_deg	5.932
r_scangle_it	4.07
r_scangle_other	4.068
r_mcangle_it	3.789
r_mcangle_other	3.788
r_scbond_it	2.975
r_scbond_other	2.973
r_mcbond_it	2.811
r_mcbond_other	2.809
r_chiral_restr_other	1.897
r_angle_refined_deg	1.85
r_angle_other_deg	1.309
r_symmetry_nbd_refined	0.327
r_nbd_other	0.232
r_nbd_refined	0.202
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.152
r_ncsr_local_group_1	0.114
r_symmetry_xyhbond_nbd_refined	0.094
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1853
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	68

Software

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