5MDS

Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi in complex with chitotetraose


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
4.3171.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 250.01α = 90
b = 145.047β = 94.8
c = 55.158γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979490DiamondI04

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
12.6125.3593.40.090.0818.42.956059
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6895.10.7770.6991.12.9

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 REPLACEMENTTHROUGHOUT5MDO2.6125.3554404165293.150.222010.221260.24749RANDOM62.644
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]
2.3-1.36-0.79-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.634
r_dihedral_angle_4_deg17.162
r_dihedral_angle_3_deg15.183
r_dihedral_angle_1_deg7.721
r_long_range_B_other3.825
r_long_range_B_refined3.823
r_scangle_other2.699
r_angle_refined_deg2.085
r_scbond_other1.752
r_scbond_it1.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.634
r_dihedral_angle_4_deg17.162
r_dihedral_angle_3_deg15.183
r_dihedral_angle_1_deg7.721
r_long_range_B_other3.825
r_long_range_B_refined3.823
r_scangle_other2.699
r_angle_refined_deg2.085
r_scbond_other1.752
r_scbond_it1.751
r_mcangle_it1.578
r_mcangle_other1.578
r_angle_other_deg1.038
r_mcbond_it0.962
r_mcbond_other0.962
r_chiral_restr0.109
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms7995
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms171

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing