9R5N | pdb_00009r5n

FKBP12 in complex with binfunctional ligand b3c 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, SITTING DROP		293	25% PEG3350, 0.2M ammonium thiocyanate, 0.1 M Tris-HCl pH 8.8

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.817	α = 90
b = 90.513	β = 90
c = 103.116	γ = 90

Symmetry
Space Group	P 21 21 21

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		2024-11-07	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	3	48.72	99.9	0.306	0.332	0.127	0.989	8.9	12.5		11367

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)
	3	3.18	100		0.66	0.713	0.269	0.936	4.3	13.2

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	3	48.72	11326	596	99.789	0.263	0.26	0.2553	0.312	0.3077	26.841

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]
-4.63			-0.726		5.356

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.593
r_dihedral_angle_3_deg	18.365
r_dihedral_angle_6_deg	14.699
r_dihedral_angle_1_deg	6.224
r_dihedral_angle_other_2_deg	3.396
r_angle_refined_deg	2.67
r_lrange_it	0.901
r_lrange_other	0.901
r_angle_other_deg	0.848
r_mcangle_it	0.826
r_mcangle_other	0.826
r_scangle_it	0.501
r_scangle_other	0.501
r_mcbond_it	0.478
r_mcbond_other	0.478
r_nbd_other	0.235
r_symmetry_nbd_other	0.232
r_nbd_refined	0.228
r_symmetry_nbd_refined	0.21
r_nbtor_refined	0.203
r_scbond_it	0.2
r_scbond_other	0.2
r_ncsr_local_group_2	0.188
r_symmetry_xyhbond_nbd_refined	0.172
r_xyhbond_nbd_refined	0.169
r_ncsr_local_group_1	0.163
r_chiral_restr	0.128
r_symmetry_nbtor_other	0.102
r_symmetry_xyhbond_nbd_other	0.072
r_bond_refined_d	0.019
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	3265
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	148

Software

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