5T4U

Crystal structure of the bromodomain of human BRPF1 in complex with a quinolinone ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LC2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	20 % PEG3350, 0.2 M ammonium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.315	α = 90
b = 60.315	β = 90
c = 63.389	γ = 120

Symmetry
Space Group	P 32 2 1

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		2014-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9686	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	1.5	27.23	100	0.072	0.024	0.998	17.8	9.5	21838	206811			18.293

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		0.35	0.939	4.9	7.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4LC2	1.5	27.23	20751	1061	99.98	0.20755	0.20634	0.23079	RANDOM	23.609

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]
-0.25	-0.13		-0.25		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.567
r_dihedral_angle_4_deg	17.165
r_dihedral_angle_3_deg	11.157
r_long_range_B_refined	5.531
r_long_range_B_other	5.423
r_dihedral_angle_1_deg	4.691
r_scangle_other	4.218
r_scbond_it	2.738
r_scbond_other	2.735
r_mcangle_other	2.3
r_mcangle_it	2.297
r_angle_refined_deg	1.656
r_mcbond_it	1.654
r_mcbond_other	1.596
r_angle_other_deg	0.856
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	934
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	16

Software

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