2A4D | pdb_00002a4d

Structure of the human ubiquitin-conjugating enzyme E2 variant 1 (UEV-1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J7D	PDB ENTRY 1J7D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	298	32% PEG1500, 0.2 M NaCl, 1 mM DTT, 0.1 M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.058	α = 90
b = 53.91	β = 90
c = 108.034	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	MIRRORS	2005-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E

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	1.69	30	96.4	0.038	44	5.9		13994		-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	1.69	1.75	96.4		0.332	2.7	2.8

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 1J7D	1.69	30	13966	13262	704	96.8	0.185	0.183	0.18	0.24	0.24	RANDOM	31.28

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]
-0.71			0.23		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.068
r_dihedral_angle_4_deg	17.991
r_dihedral_angle_3_deg	14.956
r_sphericity_free	6.923
r_scangle_it	6.073
r_dihedral_angle_1_deg	5.47
r_scbond_it	5.101
r_sphericity_bonded	4.924
r_mcangle_it	3.806
r_rigid_bond_restr	3.74
r_mcbond_it	2.869
r_angle_refined_deg	1.552
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.211
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1104
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms

Software

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