8QWT

Ligninolytic manganese peroxidase Cst-MnP1 from Agaricales mushrooms in complex with a manganese ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q3U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729520% PEG 8000, 0,1 M Tris-HCl, pH 7, 0,3M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.1643.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.79α = 90
b = 56.64β = 90
c = 109.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS 6M2019-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

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
11.556.6499.90.1140.1380.0760.9968.35.848414
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)
11.51.5399.81.1471.3890.7730.6381.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.554.75548336243299.8550.1640.16320.188816.86
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]
2.362-1.688-0.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.696
r_dihedral_angle_3_deg11.107
r_dihedral_angle_2_deg6.737
r_dihedral_angle_1_deg5.881
r_lrange_it4.429
r_lrange_other4.429
r_scangle_it3.422
r_scangle_other3.422
r_mcangle_other2.388
r_mcangle_it2.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.696
r_dihedral_angle_3_deg11.107
r_dihedral_angle_2_deg6.737
r_dihedral_angle_1_deg5.881
r_lrange_it4.429
r_lrange_other4.429
r_scangle_it3.422
r_scangle_other3.422
r_mcangle_other2.388
r_mcangle_it2.387
r_scbond_it2.344
r_scbond_other2.341
r_angle_refined_deg1.863
r_mcbond_it1.629
r_mcbond_other1.628
r_angle_other_deg0.671
r_symmetry_nbd_refined0.307
r_nbd_other0.28
r_nbd_refined0.24
r_symmetry_xyhbond_nbd_refined0.221
r_xyhbond_nbd_refined0.204
r_symmetry_nbd_other0.195
r_nbtor_refined0.18
r_chiral_restr0.093
r_metal_ion_refined0.086
r_symmetry_nbtor_other0.078
r_chiral_restr_other0.04
r_gen_planes_refined0.011
r_gen_planes_other0.011
r_bond_refined_d0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2415
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing