9GQG | pdb_00009gqg

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog m5(10,7)-(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

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.157	α = 90
b = 48.157	β = 90
c = 188.036	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 EIGER2 X 9M		2023-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.873129	ESRF	ID30B

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	188.04	99.9	0.078	0.09	0.044	0.999	11.3	7.3		17996

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	99.9		1.37	1.562	0.737	0.615	1.5	7.2

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	62.757	17932	883	99.794	0.218	0.2152	0.2161	0.2611	0.2619	44.646

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]
-1.715	-0.858		-1.715		5.564

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.605
r_dihedral_angle_3_deg	14.82
r_dihedral_angle_6_deg	14.217
r_dihedral_angle_1_deg	8.992
r_dihedral_angle_other_2_deg	8.975
r_lrange_it	7.725
r_lrange_other	7.723
r_scangle_it	6.099
r_scangle_other	6.097
r_mcangle_it	5.195
r_mcangle_other	5.193
r_scbond_it	4.531
r_scbond_other	4.528
r_mcbond_it	4.072
r_mcbond_other	4.066
r_angle_refined_deg	2.625
r_angle_other_deg	0.895
r_symmetry_nbd_refined	0.309
r_nbd_refined	0.213
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.192
r_nbd_other	0.18
r_chiral_restr	0.132
r_ncsr_local_group_1	0.117
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.108
r_symmetry_xyhbond_nbd_refined	0.068
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1819
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	82

Software

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