9GLP | pdb_00009glp

Crystal Structure of UFC1 C116E&T106I

X-RAY DIFFRACTION

---

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	293	0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.837	α = 90
b = 46.837	β = 90
c = 144.089	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	298	PIXEL	DECTRIS EIGER X 9M		2024-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	1.7	44.543	99.97	0.04144	0.999	13.74	2		16486			20.22

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	1.77	1.833	100		0.2425	0.924	3.44	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	1.77	44.543	16486	853	99.982	0.179	0.1777	0.192	0.1996	0.2042	19.787

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]
0.042			0.042		-0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.434
r_dihedral_angle_4_deg	16.714
r_dihedral_angle_3_deg	12.472
r_lrange_it	6.854
r_lrange_other	6.846
r_dihedral_angle_1_deg	6.234
r_scangle_it	4.055
r_scangle_other	4.006
r_scbond_it	2.733
r_scbond_other	2.707
r_mcangle_it	2.444
r_mcangle_other	2.443
r_mcbond_it	1.713
r_mcbond_other	1.684
r_angle_refined_deg	1.647
r_angle_other_deg	1.454
r_symmetry_nbd_refined	0.24
r_nbd_refined	0.211
r_symmetry_nbd_other	0.191
r_nbd_other	0.179
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.132
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.083
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	1329
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building