8YMI | pdb_00008ymi

BRD4-BD1 in complex with 2-{[(3S)-1-benzylpyrrolidin-3-yl]methyl}-5-methyl-7-(1-methylpyrazol-3-yl)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	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 = 45.59	α = 90
b = 46.53	β = 90
c = 62.97	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		2021-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00	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	1.01	50	99.5	0.931	10.63	15.7		70604

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	1.01	1.07			0.916

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	1.01	37.422	70533	3618	99.468	0.19	0.1885	0.1947	0.2109	0.2154	9.503

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]
-0.078			-0.021		0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.414
r_dihedral_angle_4_deg	21.909
r_dihedral_angle_3_deg	12.055
r_rigid_bond_restr	10.278
r_dihedral_angle_1_deg	5.646
r_angle_other_deg	2.204
r_angle_refined_deg	2.131
r_lrange_it	1.962
r_scangle_it	1.782
r_scangle_other	1.781
r_lrange_other	1.723
r_scbond_it	1.569
r_scbond_other	1.569
r_mcangle_other	1.379
r_mcangle_it	1.242
r_mcbond_it	1.082
r_mcbond_other	0.973
r_nbd_refined	0.238
r_nbd_other	0.237
r_symmetry_nbd_refined	0.232
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.146
r_chiral_restr	0.126
r_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.032
r_bond_refined_d	0.019
r_gen_planes_other	0.019
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1052
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	46

Software

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