3DWY | pdb_00003dwy

Crystal Structure of the Bromodomain of Human CREBBP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NXB	ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI
experimental model	PDB	2OO1	ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI
experimental model	PDB	2OSS	ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI
experimental model	PDB	2OUO	ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI
experimental model	PDB	2RFJ	ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI
experimental model	PDB	3DAI	ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2M KSCN, 25% PEG3350, 5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.484	α = 90
b = 121.484	β = 90
c = 40.378	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		2008-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.98	23.65	99.9	0.086	0.086	11.6	3.7		15467

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.09	100		0.624	0.086	2	3.6	2257

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI	1.98	23.65	15462	15460	771	99.99	0.162	0.162	0.159	0.16	0.219	0.22	RANDOM	30.488

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]
-0.93	-0.47		-0.93		1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.381
r_dihedral_angle_4_deg	19.994
r_dihedral_angle_3_deg	14.802
r_scangle_it	9.03
r_scbond_it	6.892
r_dihedral_angle_1_deg	6.082
r_mcangle_it	4.322
r_mcbond_it	3.565
r_angle_refined_deg	1.414
r_mcbond_other	1.143
r_angle_other_deg	1.087
r_symmetry_vdw_other	0.253
r_symmetry_hbond_refined	0.206
r_nbd_refined	0.195
r_nbd_other	0.187
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.141
r_nbtor_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1857
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction