2Q2I

Crystal structure of the protein secretion chaperone CsaA from Agrobacterium tumefaciens.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GD7pdb entry 1GD7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52941.8M ammonium sulfate, 0.1M HEPES pH 7.5, 2% PEG400, 5% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.448.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.653α = 90
b = 60.653β = 90
c = 113.389γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVariMax Cu HF2004-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5552.5399.80.0423.710.82341233412333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6199.60.3417.210.133400

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1GD71.5552.533409934099172799.70.180.1780.208RANDOM7.929
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]
-0.21-0.11-0.210.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.975
r_dihedral_angle_4_deg18.079
r_dihedral_angle_3_deg10.815
r_dihedral_angle_1_deg6.318
r_scangle_it2.218
r_scbond_it1.473
r_angle_refined_deg1.282
r_mcangle_it0.828
r_mcbond_it0.546
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.975
r_dihedral_angle_4_deg18.079
r_dihedral_angle_3_deg10.815
r_dihedral_angle_1_deg6.318
r_scangle_it2.218
r_scbond_it1.473
r_angle_refined_deg1.282
r_mcangle_it0.828
r_mcbond_it0.546
r_nbtor_refined0.312
r_nbd_refined0.193
r_symmetry_vdw_refined0.186
r_symmetry_hbond_refined0.118
r_xyhbond_nbd_refined0.111
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1677
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms25

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
PHASERphasing