9GLT | pdb_00009glt

Crystal Structure of Yeast Ubc13 C87E

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.603	α = 90
b = 127.663	β = 96.21
c = 42.33	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	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	1.45	42.08	98.06	0.065	0.996	11.87	2.8		46789			16.26

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	1.45	1.502	99.69		0.5799	0.737	2.6	2.9

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	1.45	42.08	46745	2339	98.074	0.193	0.1913	0.1914	0.228	0.2279	17.453

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]
0.128		0.148	-0.103		-0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.148
r_dihedral_angle_4_deg	15.746
r_dihedral_angle_3_deg	14.662
r_dihedral_angle_1_deg	6.402
r_lrange_it	5.475
r_lrange_other	5.341
r_scangle_it	4.077
r_scangle_other	4.076
r_scbond_it	2.772
r_scbond_other	2.771
r_mcangle_it	2.416
r_mcangle_other	2.415
r_angle_refined_deg	1.758
r_mcbond_it	1.672
r_mcbond_other	1.671
r_angle_other_deg	1.49
r_symmetry_nbd_refined	0.361
r_nbd_other	0.274
r_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.214
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2366
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building