2OOB | pdb_00002oob

crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UBQ	pdb entries 1UBQ, 2OOA
experimental model	PDB	2OOA	pdb entries 1UBQ, 2OOA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	0.2M calcium chloride, 0.1M sodium acetate, 20% PEG6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.608	α = 90
b = 54.784	β = 90
c = 94.621	γ = 90

Symmetry
Space Group	I 2 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++	Osmic multilayer confocal optics	2006-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	1.9	50	99.9	0.041	29.9	6.9	10581	10568	1	1

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)
	1.9	1.97	92.7		0.128	10.9	6.1	671

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 1UBQ, 2OOA	1.9	19.15	10581	10076	505	98.65	0.199	0.199	0.19658	0.2	0.25636	0.26	RANDOM	21.702

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	29.879
r_dihedral_angle_4_deg	17.774
r_dihedral_angle_3_deg	15.133
r_dihedral_angle_1_deg	6.203
r_scangle_it	4.777
r_scbond_it	2.888
r_angle_refined_deg	1.753
r_mcangle_it	1.728
r_mcbond_it	1.042
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.879
r_dihedral_angle_4_deg	17.774
r_dihedral_angle_3_deg	15.133
r_dihedral_angle_1_deg	6.203
r_scangle_it	4.777
r_scbond_it	2.888
r_angle_refined_deg	1.753
r_mcangle_it	1.728
r_mcbond_it	1.042
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.242
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.147
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	924
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms

Software

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