9GLO | pdb_00009glo

Crystal Structure of UFC1 C116E&T106S

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

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.802	α = 90
b = 46.802	β = 90
c = 144.376	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	1.53	39.27	99.99	0.02536	1	16.9	2		25209			17.17

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	1.53	1.585	100		0.1641	0.963	4.76	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	1.53	39.27	25209	1250	99.996	0.178	0.1768	0.1911	0.2077	0.2106	17.152

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]
0.193			0.193		-0.385

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.441
r_dihedral_angle_3_deg	12.385
r_dihedral_angle_4_deg	11.133
r_dihedral_angle_1_deg	6.257
r_lrange_it	5.226
r_lrange_other	5.183
r_scangle_it	4.241
r_scangle_other	4.213
r_scbond_it	3.03
r_scbond_other	3.01
r_mcangle_other	2.219
r_mcangle_it	2.215
r_angle_refined_deg	2.027
r_angle_other_deg	1.541
r_mcbond_it	1.523
r_mcbond_other	1.504
r_symmetry_nbd_refined	0.292
r_nbd_other	0.27
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.107
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1316
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
Coot	model building