5LAU

Oceanobacillus iheyensis macrodomain mutant G37V with ADPR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SPV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.2 M ammonium sulfate, 0.1 M MES pH 6.5 and 30% (w/v) PEGMME 5K
Crystal Properties
Matthews coefficientSolvent content
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.646α = 90
b = 109.646β = 90
c = 109.646γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirror2014-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9795ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.35401000.070.9522.212.24798614.15
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)
11.351.391000.4046.212

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 REPLACEMENTTHROUGHOUT1spv1.354045534242799.990.155660.154240.18206RANDOM18.227
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.089
r_sphericity_free25.803
r_dihedral_angle_3_deg10.972
r_sphericity_bonded10.449
r_dihedral_angle_4_deg7.282
r_dihedral_angle_1_deg6.392
r_long_range_B_refined3.075
r_long_range_B_other3.074
r_scangle_other2.449
r_scbond_it2.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.089
r_sphericity_free25.803
r_dihedral_angle_3_deg10.972
r_sphericity_bonded10.449
r_dihedral_angle_4_deg7.282
r_dihedral_angle_1_deg6.392
r_long_range_B_refined3.075
r_long_range_B_other3.074
r_scangle_other2.449
r_scbond_it2.018
r_scbond_other2.017
r_mcangle_it1.93
r_mcangle_other1.929
r_angle_refined_deg1.687
r_mcbond_it1.459
r_mcbond_other1.457
r_rigid_bond_restr1.234
r_angle_other_deg1.053
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms1403
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing