9GQE | pdb_00009gqe

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog m5(2,4)-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	18% PEG3350, 0.2M ammonium acetate, 0.1M HEPES-NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.71	α = 90
b = 48.71	β = 90
c = 193.946	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		2023-05-20	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	2.5	42.18	99.9	0.109	0.122	0.053	0.998	13.6	9.6		9945

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)
	2.5	2.6	100		0.417	0.459	0.19	0.955	4.9	10.7

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	2.5	42.18	9899	483	99.849	0.231	0.2282	0.2267	0.2856	0.2865	44.981

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]
-2.612	-1.306		-2.612		8.474

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.972
r_dihedral_angle_3_deg	14.734
r_dihedral_angle_6_deg	13.328
r_dihedral_angle_1_deg	9.115
r_lrange_it	3.786
r_lrange_other	3.785
r_scangle_it	2.328
r_scangle_other	2.327
r_mcangle_it	2.205
r_mcangle_other	2.204
r_angle_refined_deg	1.51
r_scbond_it	1.4
r_scbond_other	1.399
r_mcbond_it	1.361
r_mcbond_other	1.358
r_angle_other_deg	0.499
r_symmetry_xyhbond_nbd_refined	0.259
r_nbd_refined	0.203
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.168
r_xyhbond_nbd_refined	0.155
r_nbd_other	0.129
r_symmetry_nbtor_other	0.091
r_ncsr_local_group_1	0.078
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.017
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1877
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	76

Software

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