8RTR | pdb_00008rtr

Bilirubin oxidase from Myrothecium verrucaria with R356S mutation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I3J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2.5291.1520% (w/v) PEG 3350, 0.1 M malonic acid pH 2.5, protein concentration 10 mg/ml
Crystal Properties
Matthews coefficientSolvent content
3.160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.072α = 90
b = 200.888β = 90
c = 217.306γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
12.0547.785990.2240.2490.1060.98975.391634-3.723.6
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)
12.052.0999.91.7151.8990.8020.38715.4

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-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0547.78591631447998.9230.160.15980.15810.16860.20290.1803RANDOM SELECTION26.86
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]
0.477-0.203-0.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.822
r_dihedral_angle_4_deg17.948
r_dihedral_angle_3_deg12.492
r_dihedral_angle_1_deg7.811
r_lrange_it5.333
r_lrange_other5.142
r_scangle_it3.958
r_scangle_other3.958
r_scbond_it2.622
r_scbond_other2.608
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.822
r_dihedral_angle_4_deg17.948
r_dihedral_angle_3_deg12.492
r_dihedral_angle_1_deg7.811
r_lrange_it5.333
r_lrange_other5.142
r_scangle_it3.958
r_scangle_other3.958
r_scbond_it2.622
r_scbond_other2.608
r_mcangle_it2.553
r_mcangle_other2.552
r_mcbond_it1.774
r_mcbond_other1.774
r_angle_refined_deg1.651
r_angle_other_deg1.325
r_symmetry_nbd_refined0.234
r_nbd_other0.205
r_nbd_refined0.203
r_symmetry_nbd_other0.19
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.169
r_symmetry_xyhbond_nbd_refined0.148
r_symmetry_xyhbond_nbd_other0.117
r_metal_ion_refined0.094
r_symmetry_nbtor_other0.082
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8466
Nucleic Acid Atoms
Solvent Atoms1160
Heterogen Atoms255

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing