3ZDW

Substrate and dioxygen binding to the endospore coat laccase CotA from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GSKPDB ENTRY 1GSK

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.5365

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.14α = 90
b = 102.14β = 90
c = 136.85γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14ESRFID14

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
12.430.0499.90.0412.483328602

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 1GSK2.430.0631143166399.870.179420.177680.21058RANDOM23.074
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]
0.190.190.19-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.086
r_dihedral_angle_4_deg21.149
r_dihedral_angle_3_deg15.085
r_dihedral_angle_1_deg7.236
r_angle_refined_deg1.994
r_angle_other_deg0.861
r_chiral_restr0.109
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.086
r_dihedral_angle_4_deg21.149
r_dihedral_angle_3_deg15.085
r_dihedral_angle_1_deg7.236
r_angle_refined_deg1.994
r_angle_other_deg0.861
r_chiral_restr0.109
r_bond_refined_d0.02
r_gen_planes_refined0.01
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms4045
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing