6VD9

Metal-bound C-terminal domain of the CzcD transporter from Cuprividus metallidurans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2 M ammonium sulphate, 0.1 M Bis-Tris pH 5.7, 22% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3347.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.76α = 98.78
b = 39.029β = 104.76
c = 63.965γ = 90.09
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.753996.30.997.22.929396
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.780.932

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6VD81.7538.5727942145396.260.22530.22360.25808RANDOM23.929
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]
0.75-0.310.20.22-0.33-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_3_deg13.789
r_dihedral_angle_1_deg7.129
r_long_range_B_refined6.412
r_long_range_B_other6.371
r_scangle_other4.353
r_mcangle_it3.135
r_mcangle_other3.134
r_scbond_it2.985
r_scbond_other2.971
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_3_deg13.789
r_dihedral_angle_1_deg7.129
r_long_range_B_refined6.412
r_long_range_B_other6.371
r_scangle_other4.353
r_mcangle_it3.135
r_mcangle_other3.134
r_scbond_it2.985
r_scbond_other2.971
r_mcbond_it2.161
r_mcbond_other2.16
r_angle_refined_deg1.546
r_angle_other_deg1.363
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2208
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms4

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement