3BZ5

Functional domain of InlJ from Listeria monocytogenes includes a cysteine ladder


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O6V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.42982M Ammonium sulfate, 0.1M Na acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3162.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.272α = 90
b = 159.272β = 90
c = 159.272γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSi [111], horizontally focussing2006-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.817EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.721.2899.90.1120.11217.911.218505184861149.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.80.3910.3915.37.11809

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 REPLACEMENTTHROUGHOUT1O6V2.721.28185051705991997.170.185120.181520.25261RANDOM16.976
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.172
r_dihedral_angle_3_deg12.189
r_dihedral_angle_1_deg5.712
r_scangle_it4.312
r_mcangle_it3.968
r_dihedral_angle_4_deg3.287
r_mcbond_it3.151
r_scbond_it3.145
r_angle_refined_deg1.815
r_angle_other_deg1.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.172
r_dihedral_angle_3_deg12.189
r_dihedral_angle_1_deg5.712
r_scangle_it4.312
r_mcangle_it3.968
r_dihedral_angle_4_deg3.287
r_mcbond_it3.151
r_scbond_it3.145
r_angle_refined_deg1.815
r_angle_other_deg1.733
r_mcbond_other0.517
r_symmetry_vdw_refined0.212
r_nbd_refined0.172
r_symmetry_vdw_other0.154
r_nbd_other0.153
r_nbtor_refined0.142
r_xyhbond_nbd_refined0.121
r_symmetry_hbond_refined0.112
r_nbtor_other0.069
r_chiral_restr0.062
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3498
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing