3E46 | pdb_00003e46

Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington interacting protein 2) M172A mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BEP	PDB entry 2BEP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	Calcium acetate, Sodium acetate, NaCl, PEG 8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.49	α = 90
b = 134.49	β = 90
c = 38.404	γ = 90

Symmetry
Space Group	I 4

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	MARMOSAIC 300 mm CCD		2008-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97000	APS	22-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	1.86	50	93.4	0.081		4		27414		2	26

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)
	1.86	1.91	52.4		0.374	1.98	1.4	1674

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 (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 2BEP	1.86	32.38	27404	1403	93.87	0.174	0.172	0.18	0.21	0.22	RANDOM	36.498

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			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.906
r_dihedral_angle_4_deg	16.114
r_dihedral_angle_3_deg	12.945
r_dihedral_angle_1_deg	5.429
r_scangle_it	5.299
r_scbond_it	3.253
r_mcangle_it	2.099
r_angle_refined_deg	1.514
r_mcbond_it	1.361
r_angle_other_deg	0.939
r_symmetry_vdw_refined	0.32
r_metal_ion_refined	0.258
r_mcbond_other	0.252
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.208
r_nbd_other	0.201
r_symmetry_vdw_other	0.186
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.13
r_chiral_restr	0.095
r_nbtor_other	0.09
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1597
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling