5FUJ

Crystallization of a dimeric heme peroxygenase from the fungus Marasmius rotula


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YORPDB ENTRY 2YOR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.15 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, 15% PEG4000, 15% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.0239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.495α = 90
b = 75.698β = 90
c = 104.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.835099.70.0624.277.346573-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.9498.20.464.067.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2YOR1.8344.7744243232999.720.156330.154530.18975RANDOM23.834
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]
-1.37-0.752.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.976
r_dihedral_angle_4_deg19.679
r_dihedral_angle_3_deg13.464
r_dihedral_angle_1_deg7.076
r_scbond_it4.254
r_mcangle_it3.603
r_mcbond_it2.969
r_angle_refined_deg1.47
r_chiral_restr0.105
r_gen_planes_refined0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.976
r_dihedral_angle_4_deg19.679
r_dihedral_angle_3_deg13.464
r_dihedral_angle_1_deg7.076
r_scbond_it4.254
r_mcangle_it3.603
r_mcbond_it2.969
r_angle_refined_deg1.47
r_chiral_restr0.105
r_gen_planes_refined0.016
r_bond_refined_d0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3602
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms212

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing