9GPT | pdb_00009gpt

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 12c/k

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	12% PEG3350, 0.2M ammonium acetate, 0.1M HEPES-NaOH pH 7.5, 10% glycol

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.924	α = 90
b = 48.924	β = 90
c = 194.888	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		2024-03-15	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	48.72	100	0.117	0.127	0.051	0.999	12.2	11.4		19295

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	100		1.3	1.412	0.55	0.74	2	12.3

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	42.405	19232	1018	99.964	0.223	0.2205	0.2196	0.2749	0.2716	39.925

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]
-0.705	-0.352		-0.705		2.286

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.493
r_dihedral_angle_6_deg	14.865
r_dihedral_angle_3_deg	12.162
r_dihedral_angle_1_deg	8.562
r_lrange_other	6.156
r_lrange_it	6.148
r_scangle_it	3.878
r_scangle_other	3.876
r_mcangle_it	3.573
r_mcangle_other	3.572
r_scbond_it	2.707
r_scbond_other	2.705
r_mcbond_it	2.54
r_mcbond_other	2.534
r_angle_refined_deg	1.795
r_angle_other_deg	0.615
r_symmetry_xyhbond_nbd_refined	0.262
r_nbd_refined	0.203
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.171
r_symmetry_nbd_refined	0.156
r_nbd_other	0.136
r_ncsr_local_group_1	0.112
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1821
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	82

Software

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