9NO5 | pdb_00009no5

Crystal structure of vWFA domain from LapA adhesin of Pseudomonas fluorescens

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	295	PEG 8000, cacodylate, calcium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.253	α = 90
b = 84.226	β = 90
c = 96.233	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	IMAGE PLATE	RIGAKU RAXIS IV		2020-03-05	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2020-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	2.29
2	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.98400	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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
2	1.45	48.12	100	0.078	0.081	0.022	0.999	20.1	13.1		105997			13.036

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
2	1.45	1.47	100		0.941	0.306	0.867	2.6	11.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.45	48.163	105912	5261	99.993	0.171	0.1701	0.1712	0.1857	0.1868	5%	18.787

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]
1.332			-0.353		-0.979

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.894
r_dihedral_angle_3_deg	11.066
r_dihedral_angle_2_deg	6.53
r_dihedral_angle_1_deg	6.178
r_lrange_it	5.205
r_scangle_it	3.2
r_scbond_it	2.238
r_mcangle_it	2.046
r_angle_refined_deg	1.459
r_mcbond_it	1.33
r_nbtor_refined	0.309
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.134
r_ncsr_local_group_3	0.096
r_chiral_restr	0.09
r_ncsr_local_group_2	0.087
r_ncsr_local_group_1	0.075
r_metal_ion_refined	0.073
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4191
Nucleic Acid Atoms
Solvent Atoms	725
Heterogen Atoms	20

Software

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