5MDQ

Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MDO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29328% (w/v) PEG 400, 0.2 M sodium acetate, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.4572.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 255.73α = 90
b = 148.639β = 94.94
c = 54.364γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.92DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.549.1595.50.0860.07812.24.166687

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 REPLACEMENTTHROUGHOUT5MDO2.5128.3964598208995.40.230480.230130.24093RANDOM55.574
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]
-1.20.480.590.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_4_deg19.92
r_dihedral_angle_3_deg15.443
r_dihedral_angle_1_deg7.281
r_long_range_B_refined3.272
r_long_range_B_other3.251
r_scangle_other2.006
r_angle_refined_deg1.923
r_mcangle_it1.538
r_mcangle_other1.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_4_deg19.92
r_dihedral_angle_3_deg15.443
r_dihedral_angle_1_deg7.281
r_long_range_B_refined3.272
r_long_range_B_other3.251
r_scangle_other2.006
r_angle_refined_deg1.923
r_mcangle_it1.538
r_mcangle_other1.538
r_angle_other_deg1.362
r_scbond_it1.226
r_scbond_other1.226
r_mcbond_it0.921
r_mcbond_other0.921
r_chiral_restr0.116
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.009
r_gen_planes_other0.007
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 Atoms8169
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing