5MLJ | pdb_00005mlj

Bromodomain of Human GCN5 with 4-bromo-2-methyl-5-(((3R,5R)-1-methyl-5-phenylpiperidin-3-yl)amino)pyridazin-3(2H)-one

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.63	α = 90
b = 74	β = 90
c = 76.31	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		2014-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97626	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	38.84	92.8	0.043	18.2	2.6		22545

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	73		0.069	10.5	2.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	38.84	21384	1142	91.49	0.16889	0.16669	0.18	0.21101	0.22	RANDOM	17.319

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]
0.1			-0.5		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.5
r_dihedral_angle_4_deg	17.722
r_dihedral_angle_3_deg	10.196
r_dihedral_angle_1_deg	4.678
r_long_range_B_refined	4.284
r_long_range_B_other	4.283
r_scangle_other	1.863
r_mcangle_it	1.382
r_mcangle_other	1.381
r_scbond_it	1.075
r_scbond_other	1.075
r_angle_refined_deg	0.978
r_mcbond_it	0.801
r_mcbond_other	0.8
r_angle_other_deg	0.748
r_chiral_restr	0.067
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
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	1779
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	54

Software

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