9GLN | pdb_00009gln

Crystal Structure of UFC1 C116E

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, 1.8 M smmonium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.727	α = 90
b = 46.727	β = 90
c = 143.465	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	1.92	44.43	97.98	0.05498	0.998	9.8	2		12645			19.6

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	1.92	1.989	100		0.2169	0.932	3.7	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	1.92	44.43	12645	653	97.993	0.185	0.1824	0.1948	0.2274	0.2352	18.611

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]
-0.331			-0.331		0.662

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.422
r_dihedral_angle_4_deg	13.339
r_dihedral_angle_3_deg	12.646
r_dihedral_angle_1_deg	6.461
r_lrange_it	5.042
r_lrange_other	4.856
r_scangle_it	3.701
r_scangle_other	3.664
r_scbond_it	2.373
r_scbond_other	2.336
r_mcangle_it	1.968
r_mcangle_other	1.968
r_angle_refined_deg	1.538
r_angle_other_deg	1.413
r_mcbond_it	1.405
r_mcbond_other	1.401
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.208
r_nbd_other	0.196
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.151
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1322
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	17

Software

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