6HOX

Crystal structure of the binding domain of Paraclostridial Mosquitocidal Protein 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294.150.12 M Ethylene glycols, 0.1 M Buffer System 3 pH 8.5, 50 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Crystal Properties
Matthews coefficientSolvent content
2.1542.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.146α = 90
b = 38.686β = 116.74
c = 108.514γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.984ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9548.4696.90.0970.1350.0930.9958.33.531355
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95294.40.7251.0090.70.6411.63.3

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 REPLACEMENTTHROUGHOUT4KBB1.9548.4629725162996.610.177560.175830.2093RANDOM33.866
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]
0.11.55-0.53-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_4_deg16.366
r_dihedral_angle_3_deg13.172
r_dihedral_angle_1_deg7.151
r_long_range_B_refined6.461
r_long_range_B_other6.461
r_scangle_other4.668
r_mcangle_it3.614
r_mcangle_other3.613
r_scbond_it2.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_4_deg16.366
r_dihedral_angle_3_deg13.172
r_dihedral_angle_1_deg7.151
r_long_range_B_refined6.461
r_long_range_B_other6.461
r_scangle_other4.668
r_mcangle_it3.614
r_mcangle_other3.613
r_scbond_it2.941
r_scbond_other2.94
r_mcbond_it2.358
r_mcbond_other2.352
r_angle_refined_deg1.206
r_angle_other_deg0.839
r_chiral_restr0.057
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms3503
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing