6NJD | pdb_00006njd

Crystal structure of RavD (residues 1-200) from Legionella pneumophila (strain Corby) complexed with Met-1 linked di-ubiquitin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	100 mM Tris-HCl, pH 8.5, 200 mM magnesium chloride and 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.74	α = 90
b = 102.09	β = 90
c = 90.92	γ = 90

Symmetry
Space Group	P 21 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 6M		2017-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97736	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	50.01	100	0.056	0.061	0.999	17.67	6.975		87704			52.129

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.17	100		0.568	0.613	0.934	3.6	7.033

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	50.01	43764	2331	99.98	0.2142	0.2124	0.2178	0.2458	0.2518	RANDOM	60.34

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]
4.17			-2.71		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.946
r_dihedral_angle_4_deg	15.813
r_dihedral_angle_3_deg	15.18
r_dihedral_angle_1_deg	6.17
r_angle_refined_deg	1.388
r_angle_other_deg	0.894
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.946
r_dihedral_angle_4_deg	15.813
r_dihedral_angle_3_deg	15.18
r_dihedral_angle_1_deg	6.17
r_angle_refined_deg	1.388
r_angle_other_deg	0.894
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5234
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.