5MDR

Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi in complex with chitohexaose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29330% (w/v) PEG 400, 0.05 M NaCl, 0.1 M sodium citrate pH 5.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.552α = 90
b = 121.941β = 117.92
c = 147.155γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I021.007270DiamondI02

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
11.9130.0299.60.0620.056113.8357447
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)
11.91.9399.50.6820.5981.83.7

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 REPLACEMENTTHROUGHOUT5MDO1.9130.02353937347699.570.172060.171960.1835RANDOM34.555
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]
-0.36-0.271.71-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.913
r_dihedral_angle_4_deg18.198
r_dihedral_angle_3_deg11.201
r_dihedral_angle_1_deg8.976
r_long_range_B_refined7.964
r_long_range_B_other7.964
r_scangle_other2.704
r_scbond_it1.743
r_scbond_other1.743
r_angle_refined_deg1.624
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.913
r_dihedral_angle_4_deg18.198
r_dihedral_angle_3_deg11.201
r_dihedral_angle_1_deg8.976
r_long_range_B_refined7.964
r_long_range_B_other7.964
r_scangle_other2.704
r_scbond_it1.743
r_scbond_other1.743
r_angle_refined_deg1.624
r_mcangle_it1.292
r_mcangle_other1.291
r_angle_other_deg1.113
r_mcbond_it0.812
r_mcbond_other0.812
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms15990
Nucleic Acid Atoms
Solvent Atoms1748
Heterogen Atoms729

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing