6CD2

Crystal structure of the PapC usher bound to the chaperone-adhesin PapD-PapG

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VQI	2VQI, 2WMP, 1J8S, 3L48
experimental model	PDB	2WMP	2VQI, 2WMP, 1J8S, 3L48
experimental model	PDB	1J8S	2VQI, 2WMP, 1J8S, 3L48
experimental model	PDB	3L48	2VQI, 2WMP, 1J8S, 3L48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	50 mM sodium citrate pH 5.0-6.0, 50 mM lithium sulfate, 50 mM sodium sulfate and 7-14% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
5.12	75.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.303	α = 90
b = 300.71	β = 90
c = 100.515	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER X 16M		2017-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.979	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.7	50	98.5	0.122	0.134	0.054	15.9	6		27152

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.7	3.83	92.5		0.448	1.5	5.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2VQI, 2WMP, 1J8S, 3L48	3.7	50.01	25768	1384	80.96	0.28433	0.28203	0.32932	RANDOM	135.172

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]
-10.34			2.02		8.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.743
r_dihedral_angle_4_deg	15.281
r_dihedral_angle_3_deg	14.562
r_dihedral_angle_1_deg	6.705
r_long_range_B_refined	6.472
r_long_range_B_other	6.472
r_mcangle_it	2.457
r_mcangle_other	2.457
r_scangle_other	1.518
r_mcbond_it	1.333
r_mcbond_other	1.333
r_angle_refined_deg	1.26
r_angle_other_deg	0.927
r_scbond_it	0.746
r_scbond_other	0.746
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8640
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing