9P1Q | pdb_00009p1q

Crystal structure of Ube2E3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y6L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.8 M LiCl, 0.1 M Tris pH 8.5, 32%(w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.56	α = 90
b = 62.82	β = 95.46
c = 51.57	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	IMAGE PLATE	RIGAKU RAXIS IV++		2016-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5419

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.08	25.681	95.6	0.018	0.026	0.018	0.999	13842.9	1.7		17482			17.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.15	81.5		0.046	0.065	0.046	0.993	13.3	1.53

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.15	25.681	16084	1606	97.114	0.181	0.1741	0.174	0.2461	0.2458	17.729

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]
0.032		0.27	0.518		-0.591

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.245
r_dihedral_angle_3_deg	13.604
r_dihedral_angle_2_deg	10.486
r_dihedral_angle_1_deg	6.83
r_lrange_it	5.808
r_lrange_other	5.741
r_scangle_it	4.208
r_scangle_other	4.207
r_mcangle_other	2.828
r_mcangle_it	2.827
r_scbond_it	2.602
r_scbond_other	2.601
r_mcbond_it	1.834
r_mcbond_other	1.827
r_angle_refined_deg	1.779
r_angle_other_deg	0.596
r_symmetry_nbd_refined	0.357
r_nbd_other	0.349
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.206
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.174
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.009
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	2322
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms

Software

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