9FM0 | pdb_00009fm0

Human antibody (Fab) and P. aeruginosa (T3SS) protein PcrV-fragment complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	Micro-seeding, 0.1 M Sodium Acetate pH 5, 25% PEG 1000, 0.001M ZnCl2

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.582	α = 90
b = 92.308	β = 104.828
c = 105.22	γ = 90

Symmetry
Space Group	P 1 21 1

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 2M		2023-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.559	49.21	99.5	0.2	0.977	5.02	3.38		52157			45.86

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.56	2.71	99.2		1.53	0.312	0.72	3.3

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	2.56	49.21	52157	2086	99.54	0.211	0.2097	0.2159	0.237	0.2416	46.739

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]
0.306		-0.474	-0.233		0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.825
r_dihedral_angle_3_deg	11.536
r_dihedral_angle_1_deg	7.449
r_lrange_it	6.67
r_lrange_other	6.646
r_dihedral_angle_2_deg	5.495
r_scangle_it	4.588
r_scangle_other	4.588
r_mcangle_it	3.543
r_mcangle_other	3.543
r_scbond_it	2.81
r_scbond_other	2.81
r_mcbond_it	2.154
r_mcbond_other	2.152
r_angle_refined_deg	1.266
r_angle_other_deg	0.456
r_xyhbond_nbd_refined	0.243
r_nbd_refined	0.203
r_symmetry_nbd_other	0.191
r_nbd_other	0.183
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.128
r_symmetry_nbd_refined	0.109
r_symmetry_xyhbond_nbd_other	0.102
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.055
r_ncsr_local_group_3	0.051
r_ncsr_local_group_2	0.042
r_ncsr_local_group_1	0.027
r_gen_planes_refined	0.013
r_gen_planes_other	0.012
r_bond_refined_d	0.006
r_ext_dist_refined_b	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8596
Nucleic Acid Atoms
Solvent Atoms	392
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing