9QW8 | pdb_00009qw8

FKBP12 in complex with bifunctional ligand 1ad and the first bromodomain of BRD4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PPN
experimental model	PDB	7C2Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	22% PEG3350, 0.2 M NaCl, 0.1 M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.648	α = 86.458
b = 35.65	β = 84.218
c = 100.919	γ = 72.475

Symmetry
Space Group	P 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 CdTe 16M		2023-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.885603	ESRF	ID23-1

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	1.8	100.35	97	0.078	0.111	0.078	0.977	8.4	3.3		42398

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)
	1.8	1.84	94.6		0.577	0.816	0.577	0.563	1.7	3.1

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	1.8	100.35	42396	2063	97.02	0.215	0.2133	0.2137	0.2428	0.238	24.851

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]
-0.703	0.398	-0.78	-0.27	-0.216	1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.876
r_dihedral_angle_6_deg	15.179
r_dihedral_angle_3_deg	14.471
r_dihedral_angle_1_deg	7.204
r_lrange_it	4.252
r_lrange_other	4.221
r_scangle_it	2.526
r_scangle_other	2.526
r_angle_refined_deg	2.163
r_mcangle_it	1.759
r_mcangle_other	1.759
r_scbond_other	1.672
r_scbond_it	1.67
r_mcbond_it	1.23
r_mcbond_other	1.228
r_angle_other_deg	0.724
r_dihedral_angle_other_2_deg	0.646
r_symmetry_nbd_refined	0.234
r_nbd_other	0.233
r_nbd_refined	0.224
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.194
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.112
r_symmetry_xyhbond_nbd_other	0.107
r_symmetry_xyhbond_nbd_refined	0.102
r_symmetry_nbtor_other	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3652
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	138

Software

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