9GLJ | pdb_00009glj

Crystal Structure of UFC1 T106A

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	6.5	293	0.1M NaCl, 0.1M Bis-Tris pH 6.5, 1.5M Ammonium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.222	α = 90
b = 47.222	β = 90
c = 142.039	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 CdTe 16M		2022-11-10	M	SINGLE WAVELENGTH

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

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	1.213	33.43	99.99	0.022	1	15.16	2		49774			15.33

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	1.213	1.256	100		0.3448	0.836	2.32	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	1.213	33.43	49774	2494	99.998	0.178	0.1768	0.1767	0.1989	0.199	17.434

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]
-0.061			-0.061		0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.122
r_dihedral_angle_4_deg	13.406
r_dihedral_angle_3_deg	12.004
r_dihedral_angle_1_deg	6.323
r_lrange_it	4.992
r_lrange_other	4.811
r_scangle_it	4.042
r_scangle_other	4.041
r_scbond_it	2.798
r_scbond_other	2.797
r_mcangle_it	2.124
r_mcangle_other	2.124
r_angle_refined_deg	1.916
r_angle_other_deg	1.52
r_mcbond_it	1.435
r_mcbond_other	1.426
r_symmetry_nbd_refined	0.313
r_nbd_other	0.26
r_nbd_refined	0.232
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.117
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.016
r_symmetry_xyhbond_nbd_other	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1337
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms

Software

Software
Software Name	Purpose
autoPROC	data processing
autoPROC	data reduction
autoPROC	data scaling
REFMAC	refinement