5MQ6

Polycyclic Ketone Monooxygenase from the Thermophilic Fungus Thermothelomyces thermophila


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YLT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52982.7 M ammonium sulfate, 100 mM MES sodium salt pH 6.5, and 5% v/v PEG400
Crystal Properties
Matthews coefficientSolvent content
2.4952

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.2α = 90
b = 91.02β = 90
c = 133.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11ESRFID23-1

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
1275.211000.1620.9828.96.249615
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)
122.051001.2070.51.66.2

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 REPLACEMENTTHROUGHOUT2YLT275.2148005154199.980.155150.152690.23105RANDOM32.548
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]
-0.82-0.130.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.03
r_sphericity_free24.613
r_dihedral_angle_3_deg16.779
r_dihedral_angle_4_deg16.712
r_sphericity_bonded10.267
r_dihedral_angle_1_deg7.058
r_rigid_bond_restr6.759
r_long_range_B_refined5.794
r_long_range_B_other5.724
r_mcangle_other5.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.03
r_sphericity_free24.613
r_dihedral_angle_3_deg16.779
r_dihedral_angle_4_deg16.712
r_sphericity_bonded10.267
r_dihedral_angle_1_deg7.058
r_rigid_bond_restr6.759
r_long_range_B_refined5.794
r_long_range_B_other5.724
r_mcangle_other5.26
r_mcangle_it5.258
r_scangle_other5.224
r_scbond_it4.753
r_scbond_other4.753
r_mcbond_it4.572
r_mcbond_other4.558
r_angle_refined_deg2.129
r_angle_other_deg2.106
r_chiral_restr0.147
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_gen_planes_other0.01
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4965
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing