5MDP

Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form II)


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, 0.5 M potassium iodide, 0.1 M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
4.3171.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 254.761α = 90
b = 147.031β = 95.51
c = 53.759γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-01-30MSINGLE 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
13.0829.2195.70.1080.16.62.734933
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)
13.083.2338.50.410.3852.7

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 REPLACEMENTTHROUGHOUT5MDO3.08127.233200173195.480.21810.216990.23977RANDOM70.514
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]
1.55-2.13-1.740.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.068
r_dihedral_angle_4_deg18.112
r_dihedral_angle_3_deg17.537
r_dihedral_angle_1_deg8.778
r_angle_refined_deg2.17
r_long_range_B_refined1.491
r_long_range_B_other1.491
r_angle_other_deg1.256
r_scangle_other0.783
r_mcangle_it0.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.068
r_dihedral_angle_4_deg18.112
r_dihedral_angle_3_deg17.537
r_dihedral_angle_1_deg8.778
r_angle_refined_deg2.17
r_long_range_B_refined1.491
r_long_range_B_other1.491
r_angle_other_deg1.256
r_scangle_other0.783
r_mcangle_it0.753
r_mcangle_other0.753
r_scbond_it0.476
r_scbond_other0.476
r_mcbond_it0.423
r_mcbond_other0.423
r_chiral_restr0.105
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing