8YMF | pdb_00008ymf

BRD4-BD1 in complex with 7-[2-(cyclopropylmethoxy)phenyl]-5-methyl-2-[(1-methylsulfonyl-4-piperidyl)methyl]pyrazolo[4,3-c]pyridin-4-one

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	7.5	293	0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.03	α = 90
b = 52.37	β = 90
c = 57.94	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 EIGER X 16M		2020-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

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	1.015	50	79.9	0.997	16.84	3.17		99575

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	1.015	1.04	9.9		0.878

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	1.015	38.852	52990	2650	81.308	0.148	0.1473	0.1554	0.1712	0.1766	12.873

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]
0.244			-0.314		0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.573
r_dihedral_angle_4_deg	22.268
r_rigid_bond_restr	12.448
r_dihedral_angle_3_deg	11.305
r_dihedral_angle_1_deg	5.649
r_scangle_it	2.993
r_scangle_other	2.991
r_scbond_it	2.397
r_scbond_other	2.395
r_angle_other_deg	2.344
r_lrange_it	2.28
r_lrange_other	2.206
r_angle_refined_deg	2.149
r_mcangle_other	1.447
r_mcangle_it	1.425
r_mcbond_it	1.186
r_mcbond_other	1.139
r_symmetry_nbd_refined	0.288
r_nbd_refined	0.247
r_nbd_other	0.241
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.2
r_symmetry_xyhbond_nbd_refined	0.185
r_chiral_restr	0.144
r_xyhbond_nbd_refined	0.121
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.032
r_gen_planes_other	0.021
r_bond_refined_d	0.019
r_xyhbond_nbd_other	0.018
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1043
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	33

Software

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