9I9M | pdb_00009i9m

Crystal structure of chimeric UFC1, TAK MotiF replaced with HPN motif of other E2 proteins

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1M sodium citrate tribasic dihydrate pH 5.5, 20% w/v 2-propanol, 20% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.163	α = 90
b = 47.163	β = 90
c = 144.632	γ = 90

Symmetry
Space Group	P 41 21 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	PIXEL	DECTRIS EIGER2 XE 9M		2025-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.543	44.84	99.86	0.03874	0.999	12.8	2		24971			20.41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.543	1.598	98.65		0.9574	0.525	0.81	2

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	1.543	44.839	24971	1259	99.868	0.191	0.1902	0.2023	0.2088	0.2236	21.516

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]
-0.067			-0.067		0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.57
r_dihedral_angle_4_deg	19.497
r_dihedral_angle_3_deg	11.5
r_dihedral_angle_1_deg	6.564
r_lrange_it	6.25
r_lrange_other	6.177
r_scangle_it	5.138
r_scangle_other	5.135
r_scbond_it	3.454
r_scbond_other	3.452
r_mcangle_it	2.866
r_mcangle_other	2.864
r_mcbond_it	1.914
r_mcbond_other	1.914
r_angle_refined_deg	1.583
r_angle_other_deg	1.431
r_symmetry_nbd_refined	0.243
r_nbd_refined	0.213
r_symmetry_nbd_other	0.19
r_nbd_other	0.182
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.133
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1362
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
Coot	model building