2JG7

Crystal structure of Seabream Antiquitin and Elucidation of its substrate specificity

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BPW	PDB ENTRY 1BPW

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.16	α = 90.5
b = 111.02	β = 98.1
c = 113.64	γ = 111.59

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS		PAL/PLS

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	2.8	30.2	93	0.12	7.3	2.9		86382		2

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	2.8	2.9	85		0.3	2.1	2.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BPW	2.83	30.19	82050	4332	100	0.211	0.21	0.228	RANDOM	21.48

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]
-0.2	0.13	0.11	-0.46	-0.46	0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.999
r_dihedral_angle_4_deg	16.101
r_dihedral_angle_3_deg	15.112
r_dihedral_angle_1_deg	5.142
r_scangle_it	1.637
r_angle_refined_deg	1.062
r_scbond_it	0.931
r_mcangle_it	0.618
r_mcbond_it	0.358
r_nbtor_refined	0.301
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.164
r_symmetry_hbond_refined	0.126
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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_refined
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
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30944
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	352

Software

Software
Software Name	Purpose
REFMAC	refinement