9GMN | pdb_00009gmn

Crystal Structure of UFC1 T106V

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	8	293	1.5M Ammonium sulfate, 0.1M Tris pH 8.0.

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.59	α = 90
b = 46.59	β = 90
c = 142.54	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 PILATUS 200K		2022-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54187

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	2	35.63	100	0.098	0.999	13.77	6.73		20248			27.33

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	2	2.072	99.8		0.73	0.73	1.77	3.6

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	2	35.63	11313	545	100	0.18	0.1775	0.1886	0.231	0.2319	21.919

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]
-0.514			-0.514		1.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.173
r_dihedral_angle_4_deg	18.189
r_dihedral_angle_3_deg	14.277
r_dihedral_angle_1_deg	6.541
r_lrange_it	4.783
r_lrange_other	4.733
r_scangle_it	3.645
r_scangle_other	3.644
r_mcangle_it	2.353
r_mcangle_other	2.352
r_scbond_it	2.341
r_scbond_other	2.339
r_mcbond_it	1.665
r_mcbond_other	1.626
r_angle_refined_deg	1.584
r_angle_other_deg	1.344
r_nbd_other	0.219
r_symmetry_nbd_refined	0.215
r_nbd_refined	0.21
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.135
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.009
r_xyhbond_nbd_other	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1319
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling