8JNV

PfDXR - Mn2+ - MAMK89 ternary complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherdeposition is in progress

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Tris-HCl pH 8.0, 20%(w/v) PEG6000, and 0.2 M CaCl2
Crystal Properties
Matthews coefficientSolvent content
2.3647.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.637α = 90
b = 77.022β = 92.67
c = 111.275γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.663.3997.30.97410.53.311167115.15
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.630.7711.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.663.31106015568397.340.165480.163910.19428RANDOM21.958
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]
-0.68-0.480.91-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.795
r_long_range_B_refined6.741
r_long_range_B_other6.646
r_dihedral_angle_1_deg5.938
r_scangle_other5.08
r_scbond_it3.241
r_scbond_other3.24
r_mcangle_it2.836
r_mcangle_other2.836
r_dihedral_angle_2_deg2.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.795
r_long_range_B_refined6.741
r_long_range_B_other6.646
r_dihedral_angle_1_deg5.938
r_scangle_other5.08
r_scbond_it3.241
r_scbond_other3.24
r_mcangle_it2.836
r_mcangle_other2.836
r_dihedral_angle_2_deg2.615
r_angle_refined_deg2.019
r_mcbond_it1.909
r_mcbond_other1.906
r_angle_other_deg0.56
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms6570
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing