2OIV | pdb_00002oiv

Structural Analysis of Xanthomonas XopD Provides Insights Into Substrate Specificity of Ubiquitin-like Protein Proteases

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	15 mg/mL protein in 20 mM Tris-HCl pH 7.5, 75 mM KCl, and 0.5 mM DTT, 1.4 - 1.6 M sodium potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.618	α = 90
b = 91.618	β = 90
c = 44.82	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	SBC-3		2004-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97929	APS	19-BM

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	1.95	32.04	98.6	0.061	31.2	7.6	14282	14282			37.8

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	1.95	2	99.9		0.71	2.25	7.5

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 (All)	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	SAD	THROUGHOUT	1.95	32.04	14274	13554	720	100	0.21012	0.21012	0.20795	0.21	0.25017	0.26	RANDOM	42.341

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]
-1.33			-1.33		2.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.803
r_dihedral_angle_4_deg	21.515
r_dihedral_angle_3_deg	15.209
r_dihedral_angle_1_deg	6.485
r_scangle_it	3.45
r_scbond_it	2.367
r_mcangle_it	1.642
r_angle_refined_deg	1.48
r_mcbond_it	1.033
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.803
r_dihedral_angle_4_deg	21.515
r_dihedral_angle_3_deg	15.209
r_dihedral_angle_1_deg	6.485
r_scangle_it	3.45
r_scbond_it	2.367
r_mcangle_it	1.642
r_angle_refined_deg	1.48
r_mcbond_it	1.033
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.251
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.099
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1350
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	5

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.