3F92 | pdb_00003f92

Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington Interacting Protein 2) M172A mutant crystallized at pH 8.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3E46	PDB entry 3E46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	Calcium acetate, Bicine, Tris-HCl, NaCl, PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.817	α = 90
b = 134.817	β = 90
c = 38.211	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		2008-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9700	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.23	50	98.2	0.069	0.069	16.01	2.9		16794		2.39	34.057

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)
	2.23	2.31	88.8		0.377		1.9	1494

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 (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 3E46	2.23	42.64	16791	15939	852	98.19	0.174	0.172	0.18	0.213	0.22	RANDOM	34.513

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	42.445
r_dihedral_angle_4_deg	17.739
r_dihedral_angle_3_deg	15.08
r_dihedral_angle_1_deg	6.244
r_scangle_it	5.174
r_scbond_it	3.297
r_mcangle_it	2.278
r_angle_refined_deg	1.85
r_mcbond_it	1.509
r_angle_other_deg	1.078
r_mcbond_other	0.335
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.224
r_symmetry_vdw_other	0.217
r_nbd_other	0.206
r_metal_ion_refined	0.186
r_symmetry_hbond_refined	0.186
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.119
r_nbtor_other	0.092
r_symmetry_metal_ion_refined	0.075
r_bond_refined_d	0.024
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1599
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	34

Software

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