2AWF | pdb_00002awf

Structure of human Ubiquitin-conjugating enzyme E2 G1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PZV	PDB ENTRY 1PZV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	24% PEG3350, 0.2 M MgAc, 0.1 M Tris, pH 7.5, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.444	α = 90
b = 59.444	β = 90
c = 186.812	γ = 120

Symmetry
Space Group	P 61 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 4		2005-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.97985	APS	17-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	2.01	39.7	96.4	0.037	72.07	15.5	13412	13412		-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	2.01	2.08	84.6		0.647	2.25	5.2	1123

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-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 1PZV	2.1	36.98	11341	595	97.95	0.257	0.22289	0.22091	0.2235	0.26337	0.2635	RANDOM	49.808

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]
0.96	0.48		0.96		-1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.946
r_dihedral_angle_4_deg	18.492
r_dihedral_angle_3_deg	17.473
r_scangle_it	7.38
r_dihedral_angle_1_deg	6.634
r_scbond_it	4.663
r_mcangle_it	4.039
r_mcbond_it	2.605
r_angle_refined_deg	1.57
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.265
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.133
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	978
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing