9GLS | pdb_00009gls

Crystal Structure of Human UBCH5B C85E

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	9	293	10% PEG 200, 0.1 M Bis-Tris propane, pH 9, 15% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.916	α = 90
b = 49.401	β = 90
c = 63.228	γ = 90

Symmetry
Space Group	P 21 21 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	1.25	38.93	98.75	0.04743	0.998	12.33	3.7		41718			20.24

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	1.25	1.295	98.59		0.9445	0.586	1.35	3.8

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	1.25	38.928	41717	2054	98.752	0.189	0.1885	0.1983	0.2112	0.2209	21.687

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]
0.134			-0.315		0.181

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29
r_dihedral_angle_4_deg	14.236
r_dihedral_angle_3_deg	12.456
r_dihedral_angle_1_deg	6.637
r_lrange_it	5.646
r_lrange_other	5.601
r_scangle_it	4.788
r_scangle_other	4.782
r_scbond_it	3.43
r_scbond_other	3.416
r_mcangle_other	2.424
r_mcangle_it	2.414
r_angle_refined_deg	1.842
r_mcbond_it	1.715
r_mcbond_other	1.693
r_angle_other_deg	1.667
r_nbd_other	0.276
r_nbd_refined	0.221
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.173
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1168
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building