8YME | pdb_00008yme

BRD4-BD1 in complex with N-cyclohexyl-1-methyl-6-{[5-methyl-7-(1-methylpyrazol-3-yl)-4-oxo-pyrazolo[4,3-c]pyridin-2-yl]methyl}azepan-1-ium-4-carboxamide 2,2,2-trifluoroacetate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CZU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.05	α = 90
b = 49.35	β = 90
c = 61.06	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 6M		2022-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.18	50	100	0.998	10.94	14.7		43571

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.18	1.25			0.524

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	FREE R-VALUE	1.18	38.381	43508	2220	99.943	0.158	0.1567	0.1655	0.1856	0.1883	21.222

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]
0.799			-0.578		-0.221

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.447
r_dihedral_angle_4_deg	12.131
r_rigid_bond_restr	11.915
r_dihedral_angle_3_deg	11.539
r_dihedral_angle_1_deg	5.484
r_lrange_it	3.871
r_lrange_other	3.863
r_scangle_it	3.747
r_scangle_other	3.698
r_scbond_it	3.26
r_scbond_other	3.242
r_mcbond_other	2.54
r_mcbond_it	2.537
r_mcangle_it	2.489
r_mcangle_other	2.487
r_angle_other_deg	2.186
r_angle_refined_deg	1.906
r_symmetry_nbd_refined	0.347
r_nbd_other	0.28
r_nbd_refined	0.275
r_symmetry_nbd_other	0.231
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_other	0.141
r_chiral_restr	0.121
r_symmetry_nbtor_other	0.078
r_bond_other_d	0.031
r_gen_planes_other	0.02
r_bond_refined_d	0.015
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1047
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing