9GLI | pdb_00009gli

Crystal Structure of UFC1 T106C

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	7	293	1M Ammonium Citrate tribasic pH 7.0, 0.1M Bis-Tris Propane pH 7.0.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.014	α = 90
b = 47.014	β = 90
c = 142.729	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 EIGER2 XE 16M		2023-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.34767	Diamond	I03

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	1.426	44.654	96.5	0.02949	0.999	12.1	21.3		29760			15.12

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	1.426	1.451	68.6		0.8167	0.333	0.7	5

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	1.426	44.654	29636	1403	96.055	0.176	0.1745	0.1745	0.208	0.2083	16.107

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]
-0.333			-0.333		0.667

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.905
r_dihedral_angle_4_deg	14.019
r_dihedral_angle_3_deg	12.689
r_dihedral_angle_1_deg	6.577
r_lrange_it	5.061
r_lrange_other	4.853
r_scangle_it	3.895
r_scangle_other	3.893
r_scbond_it	2.602
r_scbond_other	2.6
r_mcangle_other	2.153
r_mcangle_it	2.124
r_angle_refined_deg	1.837
r_angle_other_deg	1.51
r_mcbond_it	1.501
r_mcbond_other	1.385
r_symmetry_nbd_refined	0.301
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.197
r_nbd_other	0.192
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.012
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	1358
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement