3CNR

Crystal Structure of PilZ (XAC1133) from Xanthomonas axonopodis pv citri


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829124% PEG 4000, 0.1 M Tris-HCl, 0.2 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.933.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.125α = 90
b = 62.125β = 90
c = 83.543γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-11-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX20.978294, 0.978581, 0.953724LNLSW01B-MX2

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
11.8540990.08624.710.713687
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)
1.851.9292.10.6011.745.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.935136871368773099.770.192850.190270.24345RANDOM17.861
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]
0.940.470.94-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.173
r_dihedral_angle_3_deg15.739
r_dihedral_angle_4_deg13.979
r_dihedral_angle_1_deg5.69
r_scangle_it2.43
r_scbond_it1.821
r_angle_refined_deg1.547
r_mcangle_it1.163
r_mcbond_it0.782
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.173
r_dihedral_angle_3_deg15.739
r_dihedral_angle_4_deg13.979
r_dihedral_angle_1_deg5.69
r_scangle_it2.43
r_scbond_it1.821
r_angle_refined_deg1.547
r_mcangle_it1.163
r_mcbond_it0.782
r_nbtor_refined0.317
r_nbd_refined0.238
r_symmetry_hbond_refined0.219
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.166
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1433
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing