5I3L | pdb_00005i3l

DPF3b in complex with H3K14ac peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V43	unpublished model, ultimately derived from PDB entry 3V43.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	1.4 M sodium citrate, 0.1 M HEPES, 5% MPD

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.822	α = 90
b = 121.641	β = 90
c = 56.446	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315r		2014-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.28215	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.85	50.01	100	0.102	0.11	0.041	0.998	17.7	7.1		29753

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	100		1.125	1.214	0.453	0.717	2	7.1	1817

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X-RAY DIFFRACTION		THROUGHOUT	unpublished model, ultimately derived from PDB entry 3V43.	1.85	50.01	28115	1624	99.87	0.1833	0.1817	0.1988	0.2117	0.2249	thin shells (sftools)	34.598

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]
-2.21			0.42		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.475
r_dihedral_angle_3_deg	13.934
r_dihedral_angle_4_deg	12.861
r_dihedral_angle_1_deg	6.31
r_mcangle_it	2.328
r_angle_refined_deg	1.682
r_mcbond_it	1.578
r_mcbond_other	1.576
r_angle_other_deg	1.153
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1837
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	45

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing