9GQK | pdb_00009gqk

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog m5(11,5)-(E)-OH

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, 10% glycol

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.056	α = 90
b = 49.056	β = 90
c = 196.83	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		2024-06-26	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	1.7	42.48	99.2	0.053	0.058	0.023	1	18.8	10.8		31151

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)
	1.7	1.73	90.2		1.406	1.667	0.871	0.407	1.1	6.2

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	1.7	42.48	31045	1500	98.989	0.242	0.2398	0.238	0.2874	0.2875	43.353

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]
-0.342	-0.171		-0.342		1.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.432
r_dihedral_angle_6_deg	15.95
r_dihedral_angle_3_deg	13.528
r_dihedral_angle_1_deg	8.824
r_lrange_it	5.678
r_lrange_other	5.657
r_scangle_it	4.188
r_scangle_other	4.187
r_mcangle_it	3.521
r_mcangle_other	3.52
r_scbond_it	3.19
r_scbond_other	3.189
r_mcbond_it	2.863
r_mcbond_other	2.863
r_angle_refined_deg	2.413
r_dihedral_angle_other_2_deg	1.802
r_angle_other_deg	0.808
r_nbd_refined	0.214
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.156
r_nbd_other	0.146
r_symmetry_xyhbond_nbd_other	0.138
r_ncsr_local_group_1	0.132
r_chiral_restr	0.121
r_symmetry_nbd_refined	0.115
r_symmetry_nbtor_other	0.099
r_symmetry_xyhbond_nbd_refined	0.058
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	91
Heterogen Atoms	80

Software

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