9JOB

PfDXR - Mn2+ - NADPH - MAMK89 quaternary complex


X-RAY DIFFRACTION

Starting Model(s)

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

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
238.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.518α = 90
b = 78.201β = 92.64
c = 111.144γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

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
11.3963.9392.70.0660.0720.0280.99810.96.316400617.14
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)
11.391.410.971.1160.5370.5821.2

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 SYNTHESISTHROUGHOUT1.3963.93155538839192.620.166320.165120.18919RANDOM23.431
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]
0.22-0.420.3-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.643
r_dihedral_angle_2_deg7.281
r_long_range_B_refined6.55
r_long_range_B_other6.471
r_dihedral_angle_1_deg6.029
r_scangle_other4.982
r_scbond_it3.289
r_scbond_other3.289
r_mcangle_it3.063
r_mcangle_other3.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.643
r_dihedral_angle_2_deg7.281
r_long_range_B_refined6.55
r_long_range_B_other6.471
r_dihedral_angle_1_deg6.029
r_scangle_other4.982
r_scbond_it3.289
r_scbond_other3.289
r_mcangle_it3.063
r_mcangle_other3.063
r_mcbond_it2.143
r_mcbond_other2.142
r_angle_refined_deg2.042
r_angle_other_deg0.649
r_chiral_restr0.102
r_bond_refined_d0.012
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 Atoms659
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing