8B9X | pdb_00008b9x

Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		Alphafold model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Sodium acetate trihydrate Ammonium tartrate dibasic

Crystal Properties
Matthews coefficient	Solvent content
4.42	72.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.568	α = 90
b = 145.568	β = 90
c = 83.175	γ = 120

Symmetry
Space Group	P 64

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 EIGER X 4M		2022-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	3.066	63.112	99.8	0.997	8.7	5.9		18967

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	3.066	3.28			0.446

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	Alphafold model	3.066	63.112	18956	936	99.716	0.235	0.2326	0.23	0.2723	0.27	123.573

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]
-1.579	-0.789		-1.579		5.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.225
r_dihedral_angle_4_deg	23.791
r_lrange_it	16.847
r_scangle_it	14.93
r_dihedral_angle_3_deg	13.957
r_mcangle_it	11.77
r_scbond_it	10.824
r_mcbond_it	8.713
r_dihedral_angle_1_deg	6.158
r_angle_refined_deg	1.744
r_symmetry_nbd_refined	0.376
r_nbtor_refined	0.283
r_symmetry_xyhbond_nbd_refined	0.22
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.155
r_ncsr_local_group_1	0.1
r_chiral_restr	0.059
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4041
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing
PARROT	phasing
Coot	model building