9JOA

PfDXR - Mn2+ - MAMK89 ternary complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8JNV 

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
1.9837.87

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-5A1Photon FactoryBL-5A

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
11.563.31970.0570.070.0390.98411.63.313494414.6
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)
11.51.530.6570.8060.460.5281

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 SYNTHESISTHROUGHOUT1.563.31128254668696.970.172480.171030.20052RANDOM22.324
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]
-0.45-0.350.65-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.795
r_long_range_B_refined6.73
r_long_range_B_other6.658
r_dihedral_angle_1_deg5.954
r_scangle_other4.889
r_scbond_it3.108
r_scbond_other3.107
r_mcangle_it2.755
r_mcangle_other2.755
r_dihedral_angle_2_deg2.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.795
r_long_range_B_refined6.73
r_long_range_B_other6.658
r_dihedral_angle_1_deg5.954
r_scangle_other4.889
r_scbond_it3.108
r_scbond_other3.107
r_mcangle_it2.755
r_mcangle_other2.755
r_dihedral_angle_2_deg2.318
r_mcbond_it1.867
r_mcbond_other1.866
r_angle_refined_deg1.859
r_angle_other_deg0.623
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms582
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing