9I9O | pdb_00009i9o

Crystal Structure of UFC1 K108M

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	298	0.15M Ammonium sulfate, 0.1M Sodium Hepes pH 7.0, 20%w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.21	α = 90
b = 47.21	β = 90
c = 143	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	100	PIXEL	DECTRIS PILATUS 200K		2023-08-24	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	2.051	19.706	99.47	0.101	0.996	9.68	2		10757			20.85

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	2.051	2.125	96.52		0.659	0.648	1.38	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	2.051	19.706	10757	530	99.473	0.218	0.2161	0.2238	0.2533	0.2643	20.842

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]
-0.411			-0.411		0.821

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.116
r_dihedral_angle_4_deg	22.062
r_dihedral_angle_3_deg	16.741
r_dihedral_angle_1_deg	6.01
r_lrange_it	5.379
r_lrange_other	5.376
r_scangle_it	2.911
r_scangle_other	2.91
r_mcangle_it	2.157
r_mcangle_other	2.157
r_scbond_it	1.855
r_scbond_other	1.855
r_mcbond_it	1.401
r_mcbond_other	1.387
r_angle_other_deg	1.365
r_angle_refined_deg	1.331
r_symmetry_nbd_refined	0.325
r_symmetry_xyhbond_nbd_refined	0.312
r_nbd_other	0.249
r_symmetry_nbd_other	0.213
r_nbd_refined	0.201
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.076
r_xyhbond_nbd_other	0.018
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1347
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

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