9EMK | pdb_00009emk

DupA from legionella covalently bound to ubiquitin-based probe

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RYB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.808	α = 90
b = 86.808	β = 90
c = 146.539	γ = 120

Symmetry
Space Group	P 32

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 2M		2022-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim 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	2.17	75.3	100	0.043	0.998	10.7	5		65360

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.22	100		0.763	0.388	0.9	4.9

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	2.17	75.291	65309	3239	99.988	0.188	0.185	0.1902	0.2389	0.2488	65.654

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]
-0.174	-0.087		-0.174		0.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.51
r_dihedral_angle_6_deg	15.008
r_dihedral_angle_2_deg	10.822
r_lrange_other	7.979
r_lrange_it	7.976
r_dihedral_angle_1_deg	7.411
r_scangle_it	5.447
r_scangle_other	5.447
r_mcangle_it	3.952
r_mcangle_other	3.951
r_scbond_it	3.846
r_scbond_other	3.846
r_mcbond_it	2.711
r_mcbond_other	2.71
r_angle_refined_deg	1.835
r_angle_other_deg	0.653
r_symmetry_nbd_refined	0.264
r_nbd_other	0.261
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_refined	0.223
r_chiral_restr	0.208
r_symmetry_nbd_other	0.201
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.185
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.052
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9221
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	69

Software

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