9I9N | pdb_00009i9n

Crystal Structure of UFC1 C116E & K108A

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		298	0.1M Tris pH 8.0, 2M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.458	α = 90
b = 46.458	β = 90
c = 143.776	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 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	1.88	44.21	92.84	0.03682	0.999	15.5	2		12610			23.02

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	1.88	1.947			0.3467	0.806	2.07

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	1.88	44.208	12610	601	92.83	0.182	0.1793	0.1904	0.2288	0.2395	21.539

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]
0.014			0.014		-0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.307
r_dihedral_angle_4_deg	16.338
r_dihedral_angle_3_deg	13.138
r_dihedral_angle_1_deg	6.607
r_lrange_it	5.361
r_lrange_other	5.319
r_scangle_it	4.053
r_scangle_other	4.009
r_scbond_it	2.668
r_scbond_other	2.642
r_mcangle_it	2.218
r_mcangle_other	2.217
r_mcbond_it	1.634
r_mcbond_other	1.599
r_angle_refined_deg	1.525
r_angle_other_deg	1.394
r_nbd_refined	0.209
r_symmetry_nbd_refined	0.207
r_symmetry_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.172
r_nbd_other	0.169
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1317
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
EDNA	data collection
autoPROC	data scaling
Coot	model building