1Z2U

The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QCQ	pdb entry 1qcq

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	capillary counter-diffusion	5	277.5	7mg/mL protein in 2mM sodium citrate, 10% (v/v) ethanol, 1.5M Sodium Chloride, pH 5.0, capillary counter-diffusion, temperature 277.5K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.604	α = 90
b = 60.457	β = 106.45
c = 43.98	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MAR CCD 165 mm		2002-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97	APS	22-ID

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	1.1	30	97.4	0.055		5.5		58674

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	1.14	92.6		0.143		3	5541

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1qcq	1.1	30	57952	5900	96.162	0.132	0.1305	0.1493	RANDOM	7.614

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]
0.264		-0.109	0.037		-0.362

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.045
r_dihedral_angle_1_deg	14.377
r_dihedral_angle_4_deg	13.566
r_dihedral_angle_3_deg	12.506
r_sphericity_free	6.899
r_scangle_it	3.151
r_sphericity_bonded	2.914
r_mcangle_it	2.548
r_scbond_it	2.292
r_mcbond_it	1.724
r_scangle_other	1.639
r_mcangle_other	1.588
r_angle_refined_deg	1.335
r_rigid_bond_restr	1.206
r_scbond_other	1.041
r_angle_other_deg	0.889
r_mcbond_other	0.873
r_symmetry_vdw_refined	0.386
r_symmetry_vdw_other	0.221
r_nbd_refined	0.216
r_nbtor_refined	0.188
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.111
r_metal_ion_refined	0.111
r_chiral_restr	0.086
r_nbtor_other	0.086
r_symmetry_hbond_refined	0.047
r_symmetry_metal_ion_refined	0.024
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1175
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALEPACK	data scaling
MAR345	data collection
CNS	phasing