5FE9 | pdb_00005fe9

Crystal structure of human PCAF bromodomain in complex with compound SL1122 (compound 13)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GG3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.076	α = 90
b = 100.076	β = 90
c = 99.821	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Bruker Platinum 135		2012-01-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54167

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	2.35	32.72	99.8	0.076	14.4	5.6		15504			47.5

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	2.35	2.48	98.8		0.622	2	4.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3GG3	2.35	32.72	14724	776	99.77	0.20365	0.20094	0.2	0.25828	0.26	RANDOM	55.817

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]
-0.01			-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.882
r_dihedral_angle_4_deg	24.764
r_dihedral_angle_3_deg	15.239
r_long_range_B_refined	6.258
r_long_range_B_other	6.256
r_dihedral_angle_1_deg	5.704
r_scangle_other	2.877
r_mcangle_it	2.179
r_mcangle_other	2.178
r_scbond_it	1.722
r_scbond_other	1.721
r_angle_refined_deg	1.337
r_mcbond_it	1.286
r_mcbond_other	1.285
r_angle_other_deg	1.183
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.006
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	1805
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
SCALA	data scaling
PHASER	phasing