9GLR | pdb_00009glr

Crystal Structure of Human UBC9 C93E

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	293	2% tacsimate, pH 5.0, 0.1 M sodium citrate, 16% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.503	α = 90
b = 96.65	β = 90
c = 109.578	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	298	PIXEL	DECTRIS EIGER2 X 9M		2024-02-21	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	1.72	48.33	96.55	0.03379	0.999	12.65	1.9		19263			31.99

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	1.72	1.782	98.71		0.6958	0.645	1.31	1.9

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	1.72	48.33	19263	964	96.561	0.2	0.1988	0.2071	0.227	0.2317	33.42

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]
0.762			-1.661		0.899

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.971
r_dihedral_angle_4_deg	14.454
r_dihedral_angle_3_deg	13.83
r_lrange_it	7.155
r_lrange_other	7.117
r_dihedral_angle_1_deg	6.417
r_scangle_it	5.688
r_scangle_other	5.68
r_scbond_it	3.825
r_scbond_other	3.784
r_mcangle_other	3.682
r_mcangle_it	3.68
r_mcbond_it	2.65
r_mcbond_other	2.638
r_angle_refined_deg	1.538
r_angle_other_deg	1.315
r_nbd_refined	0.219
r_nbd_other	0.2
r_symmetry_nbd_other	0.185
r_symmetry_nbd_refined	0.176
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.164
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1247
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building