8BPT

Crystal structure of the second bromodomain of BRD5 from Leishmania donovani

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.1 M HEPES pH 7.5 and 1.4 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.37	α = 90
b = 75.356	β = 90
c = 105.798	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 PILATUS 6M-F		2018-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.6	31.845	98.3	0.047	0.054	0.025	0.999	19.4	8.1		35399

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	1.6	1.63			0.568	0.646	0.304	0.928		8.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5TCK	1.6	31.845	35358	1701	97.893	0.164	0.1615	0.2147	17.081

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]
2.076			-2.183		0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.436
r_dihedral_angle_3_deg	15.855
r_dihedral_angle_2_deg	11.057
r_dihedral_angle_1_deg	4.694
r_scangle_it	4.371
r_scangle_other	4.37
r_rigid_bond_restr	4.154
r_lrange_it	4.153
r_lrange_other	4.13
r_scbond_it	3.951
r_scbond_other	3.945
r_mcangle_it	3.278
r_mcangle_other	3.277
r_mcbond_it	2.77
r_mcbond_other	2.768
r_angle_refined_deg	1.402
r_symmetry_nbd_refined	0.78
r_angle_other_deg	0.493
r_nbd_other	0.386
r_nbd_refined	0.229
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.172
r_symmetry_xyhbond_nbd_other	0.122
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2212
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
pointless	data scaling
Coot	model building