2OB4 | pdb_00002ob4

Human Ubiquitin-Conjugating Enzyme CDC34

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	The protein was dissolved at 42 mg/ml in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol and 2 mM DTT. Crystals were grown in hanging drops by mixing 2 microL protein solution with 2 microL well solution (28% PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, 1 mM DTT and 7.5 mM glycyl-glycyl-glycine) at 21 deg C. For cryoprotection, the crystals were soaked in the well solution supplemented with 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.28	α = 90
b = 66.31	β = 90
c = 124.61	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	CCD	ADSC QUANTUM 210	cylindrically bent ULE glass mirror with Pt and Pd coatings	2005-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.97917	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	50	99.5	0.076	2.64	1.82	7162	7162		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.45	94.8		0.32	2.6	1.6	417

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	40.03	6802	6802	359	100	0.22637	0.22637	0.22323	0.2219	0.28448	0.2926	RANDOM	27.773

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]
-0.26			2.58		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.338
r_dihedral_angle_3_deg	19.471
r_dihedral_angle_4_deg	15.466
r_dihedral_angle_1_deg	6.648
r_scangle_it	2.15
r_angle_refined_deg	1.41
r_scbond_it	1.267
r_mcangle_it	1.012
r_mcbond_it	0.553
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.287
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1274
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms

Software

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