9GMM | pdb_00009gmm

Crystal Structure of UFC1 T106I

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	1.5M Ammonium sulfate, 0.1M Bis-Tris Propane pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.653	α = 90
b = 48.002	β = 90
c = 82.58	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.91976	ESRF	ID30B

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	1.35	29.4	97.43	0.066	0.997	7.8	1.83		36233			19.12

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	1.35	1.398	96.09		1.179	0.467	0.86	3

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	1.35	29.399	36233	1148	97.218	0.183	0.1822	0.1889	0.201	0.2063	21.324

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]
0.59			0.336		-0.926

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.505
r_dihedral_angle_4_deg	13.875
r_dihedral_angle_3_deg	12.714
r_dihedral_angle_1_deg	6.686
r_lrange_it	6.002
r_lrange_other	5.834
r_scangle_it	4.654
r_scangle_other	4.652
r_scbond_it	3.132
r_scbond_other	3.13
r_mcangle_it	2.616
r_mcangle_other	2.615
r_angle_refined_deg	1.846
r_mcbond_it	1.766
r_mcbond_other	1.763
r_angle_other_deg	1.522
r_symmetry_nbd_refined	0.337
r_nbd_other	0.33
r_nbd_refined	0.243
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.117
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.013
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	1357
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building