8C0D | pdb_00008c0d

UFL1/DDRGK1 bound to UFC1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EVX	for UFC1
other	AlphaFold		for UFL1 and UFBP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	292	0.1M HEPES, 1.03M Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.21	α = 90
b = 124.565	β = 90
c = 131.292	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	100	PIXEL	DECTRIS PILATUS3 X 2M		2022-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.564	65.732	93.8	0.997	8.2	12.8		25858

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.564	2.892			0.674

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	2.564	65.732	25858	1222	60.97	0.235	0.232	0.23	0.2858	0.29	47.927

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]
-1.116			1.319		-0.203

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.53
r_dihedral_angle_6_deg	16.81
r_dihedral_angle_2_deg	14.431
r_lrange_it	7.918
r_lrange_other	7.918
r_dihedral_angle_1_deg	6.066
r_scangle_it	5.348
r_scangle_other	5.347
r_mcangle_it	4.215
r_mcangle_other	4.215
r_scbond_it	3.353
r_scbond_other	3.353
r_mcbond_it	2.656
r_mcbond_other	2.656
r_angle_refined_deg	1.888
r_angle_other_deg	0.595
r_nbd_refined	0.244
r_nbd_other	0.217
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.185
r_symmetry_nbd_refined	0.164
r_xyhbond_nbd_refined	0.13
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6511
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing