3LMN | pdb_00003lmn

Oligomeric structure of the DUSP domain of human USP15

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.8	291.1	Crystals of the dusp domain of usp15 were grown at 291.1 K using the sitting drop method by mixing equal volumes of protein solution (15 mg/ml) and crystallization buffer (2.0 M ammonium formate, 0.1 M sodium acetate, pH 3.8.) The crystals were cryoprotected by immersion in well solution supplemented with 20% (v/v) glycerol prior to dunking and storage in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
4.75	73.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.174	α = 90
b = 138.174	β = 90
c = 132.114	γ = 90

Symmetry
Space Group	I 41 2 2

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		2010-01-07	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 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	2.15	20	100	0.083	35.89	14.3	35029	35029		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.19	100		0.8	3.62	14.3	1727

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 ENTRY 3JYU	2.15	19.52	33132	1749	99.95	0.18442	0.18337	0.18	0.20401	0.2	RANDOM	41.241

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.148
r_dihedral_angle_4_deg	23.241
r_dihedral_angle_3_deg	13.805
r_dihedral_angle_1_deg	5.518
r_scangle_it	2.848
r_scbond_it	1.877
r_angle_refined_deg	1.209
r_mcangle_it	1.04
r_mcbond_it	0.555
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2116
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	7

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling