8V7P

Crystal structure of the truncated P1 pilin from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-A3RJ49-F1Model was split into compact region using pLDDT scores and the "Process Predicted Models" tool on ccp4i2 (1 and 14-18, 2-13 and 79-90 and 105-124, 19-48, 49-64 and 75-78, 65-74 and 92-104)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229335% PEG8000, 100 mM sodium cacodylate, 200 mM sodium chloride
Crystal Properties
Matthews coefficientSolvent content
1.7730.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 22.453α = 90
b = 54.853β = 96.145
c = 37.772γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.0236ALS8.3.1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
10.9454.999.50.1410.1580.0690.98814.242234410.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3399.20.4980.6150.3550.6393.92.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.337.5552232468299.4920.1320.13060.1738Random10.936
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]
-0.1340.2090.33-0.236
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it15.118
r_dihedral_angle_6_deg14.375
r_lrange_other13.032
r_dihedral_angle_2_deg11.78
r_dihedral_angle_3_deg11.033
r_scangle_it6.883
r_scangle_other6.878
r_dihedral_angle_1_deg5.917
r_scbond_it4.751
r_scbond_other4.746
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it15.118
r_dihedral_angle_6_deg14.375
r_lrange_other13.032
r_dihedral_angle_2_deg11.78
r_dihedral_angle_3_deg11.033
r_scangle_it6.883
r_scangle_other6.878
r_dihedral_angle_1_deg5.917
r_scbond_it4.751
r_scbond_other4.746
r_mcangle_it4.7
r_mcangle_other4.697
r_rigid_bond_restr3.812
r_mcbond_it3.201
r_mcbond_other3.199
r_angle_refined_deg1.916
r_angle_other_deg0.664
r_nbd_other0.269
r_xyhbond_nbd_refined0.261
r_nbd_refined0.227
r_symmetry_nbd_other0.21
r_symmetry_nbd_refined0.19
r_symmetry_xyhbond_nbd_refined0.189
r_nbtor_refined0.167
r_symmetry_xyhbond_nbd_other0.167
r_chiral_restr0.1
r_symmetry_nbtor_other0.082
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms915
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing