3ZNX | pdb_00003znx

Crystal structure of the OTU domain of OTULIN D336A mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		100 MM MES/IMIDAZOLE PH 6.5, 30 MM MGCL2, 30 MM CACL2, 10% PEG 4,000, 20% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.807	α = 90
b = 72.197	β = 90
c = 94.843	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	287	CCD	ADSC QUANTUM 315r	MIRROR	2012-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.35	47.42	100	0.09	9.9	6.1		66908		3

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	1.35	1.37	100		0.7	2.4	4.7

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 3ZNV	1.35	47.47	63440	3382	99.94	0.12349	0.12163	0.1366	0.15894	0.1659	RANDOM	18.363

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]
0.37			-0.4		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.837
r_dihedral_angle_4_deg	21.292
r_sphericity_bonded	20.514
r_dihedral_angle_3_deg	12.849
r_rigid_bond_restr	10.739
r_scangle_it	6.607
r_scbond_it	5.721
r_dihedral_angle_1_deg	5.628
r_mcangle_it	3.734
r_mcbond_it	3.222
r_mcbond_other	3.206
r_angle_refined_deg	1.462
r_angle_other_deg	1
r_symmetry_vdw_refined	0.354
r_xyhbond_nbd_other	0.353
r_nbd_refined	0.347
r_xyhbond_nbd_refined	0.311
r_symmetry_vdw_other	0.228
r_nbd_other	0.222
r_nbtor_refined	0.19
r_chiral_restr	0.102
r_metal_ion_refined	0.097
r_nbtor_other	0.085
r_symmetry_hbond_refined	0.059
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2094
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling