9QD8 | pdb_00009qd8

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 29a

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	16% PEG3350, 0.1 HEPES-NaOH pH 7.5, 0.2 M ammonium acetate 10% Glycol

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.919	α = 90
b = 48.919	β = 90
c = 196.163	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	2.05	49.04	100	0.094	0.104	0.043	0.999	13.7	10.5		18036

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)
	2.05	2.11	100		1.339	1.473	0.61	0.718	2	10.9

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	2.05	38.922	17972	874	99.917	0.213	0.2107	0.2104	0.2651	0.2673	47.018

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]
-0.755	-0.378		-0.755		2.451

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.607
r_dihedral_angle_3_deg	15.243
r_dihedral_angle_6_deg	14.984
r_dihedral_angle_1_deg	8.791
r_lrange_other	6.801
r_lrange_it	6.797
r_scangle_it	5.114
r_scangle_other	5.112
r_mcangle_it	4.356
r_mcangle_other	4.355
r_scbond_it	3.662
r_scbond_other	3.66
r_mcbond_it	3.368
r_mcbond_other	3.358
r_angle_refined_deg	2.198
r_angle_other_deg	0.717
r_symmetry_nbd_refined	0.469
r_nbd_refined	0.216
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.157
r_nbd_other	0.15
r_ncsr_local_group_1	0.118
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.095
r_symmetry_xyhbond_nbd_refined	0.076
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1890
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	70

Software

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