5FE2 | pdb_00005fe2

Crystal structure of human PCAF bromodomain in complex with fragment BR013 (fragment 3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GG3	pdb id 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
3.37	63.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.45	α = 90
b = 99.45	β = 90
c = 100.51	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	IMAGE PLATE	RIGAKU RAXIS IV		2011-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	2.25	33.5	100	0.085	11.9	4.1		17600			44.5

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	2.25	2.37	100		0.644	2.1	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 (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	pdb id 3GG3	2.25	30.97	16704	892	99.96	0.20819	0.2067	0.21	0.23651	0.24	RANDOM	47.21

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]
-0.07	-0.04		-0.07		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.864
r_dihedral_angle_4_deg	18.255
r_dihedral_angle_3_deg	13.369
r_dihedral_angle_1_deg	5.702
r_long_range_B_refined	5.652
r_long_range_B_other	5.65
r_scangle_other	3.253
r_mcangle_it	2.575
r_mcangle_other	2.574
r_scbond_it	1.92
r_scbond_other	1.92
r_mcbond_it	1.544
r_mcbond_other	1.519
r_angle_refined_deg	1.485
r_angle_other_deg	1.337
r_chiral_restr	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.007
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	1778
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	38

Software

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