5MHU

The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The third structure of the series with total exposition time 63 min.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E9N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4294Protein solution (12mg/ml, 002M K-phosphate buffer, pH 6.5). Reservoir solution (0.1M citrate-phosphate buffer pH4.0, 0.2M ammonium acetat, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5150.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.39α = 90
b = 84.41β = 90
c = 112.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.81230EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.3567.5298.80.0480.99919.493.1116957-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.498.50.3130.8964.663

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 REPLACEMENTTHROUGHOUT5E9N1.3567.52111101585698.810.13430.133340.15236RANDOM10.794
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]
0.10.01-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.604
r_dihedral_angle_4_deg21.367
r_dihedral_angle_3_deg11.338
r_dihedral_angle_1_deg7.169
r_long_range_B_refined4.583
r_sphericity_bonded4.162
r_long_range_B_other3.95
r_scangle_other2.325
r_angle_refined_deg2.023
r_scbond_it1.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.604
r_dihedral_angle_4_deg21.367
r_dihedral_angle_3_deg11.338
r_dihedral_angle_1_deg7.169
r_long_range_B_refined4.583
r_sphericity_bonded4.162
r_long_range_B_other3.95
r_scangle_other2.325
r_angle_refined_deg2.023
r_scbond_it1.653
r_mcangle_it1.581
r_scbond_other1.565
r_mcangle_other1.506
r_mcbond_it1.074
r_mcbond_other1.024
r_angle_other_deg0.916
r_chiral_restr0.134
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3775
Nucleic Acid Atoms
Solvent Atoms682
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing