2OIX | pdb_00002oix

Xanthomonas XopD C470A Mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OIV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529815 mg/mL protein in 20 mM Tris-HCl pH 7.5, 75 mM KCl, and 0.5 mM DTT and 1.4 - 1.6 M sodium potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2946.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.953α = 90
b = 91.953β = 90
c = 45.013γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32005-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97905APS19-BM

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
11.825.3394.20.07530.67.6173461734630.5
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)
11.81.8477.40.581.953.1

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 (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2OIV1.825.3317317168045131000.211910.211910.210470.210.259030.27RANDOM33.158
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]
-1.75-1.753.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.339
r_dihedral_angle_4_deg20.876
r_dihedral_angle_3_deg14.385
r_dihedral_angle_1_deg5.576
r_scangle_it3.468
r_scbond_it2.377
r_mcangle_it1.703
r_angle_refined_deg1.574
r_mcbond_it1.084
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.339
r_dihedral_angle_4_deg20.876
r_dihedral_angle_3_deg14.385
r_dihedral_angle_1_deg5.576
r_scangle_it3.468
r_scbond_it2.377
r_mcangle_it1.703
r_angle_refined_deg1.574
r_mcbond_it1.084
r_nbtor_refined0.307
r_nbd_refined0.2
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.133
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.007
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 Atoms1408
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing