2ZNR

Crystal structure of the DUB domain of human AMSH-LP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	45mM sodium acetate buffer (pH 4.6), 22% PEG 4000, 90mM ammonium acetate, 10mM praseodymium (III) acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.865	α = 90
b = 81.865	β = 90
c = 64.693	γ = 120

Symmetry
Space Group	P 65

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 210	mirrors	2008-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.00000	Photon Factory	AR-NW12A

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	1.2	70.89	99.4	0.046	34.3		76845	76845

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	1.21	98.3		0.158	14.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.2	31.09	76845	72536	3830	99.37	0.14962	0.14879	0.16546	RANDOM	13.235

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]
0.57	0.29		0.57		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.57
r_dihedral_angle_3_deg	11.334
r_dihedral_angle_4_deg	8.306
r_dihedral_angle_1_deg	5.972
r_sphericity_free	4.374
r_sphericity_bonded	4.158
r_scangle_it	3.012
r_scbond_it	2.165
r_mcangle_it	1.817
r_angle_refined_deg	1.261
r_rigid_bond_restr	1.249
r_mcbond_it	1.215
r_nbtor_refined	0.307
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.196
r_symmetry_vdw_refined	0.192
r_chiral_restr	0.081
r_symmetry_hbond_refined	0.076
r_metal_ion_refined	0.053
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1432
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing