5LCC

Oceanobacillus iheyensis macrodomain mutant D40A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M magnesium formate, 20% (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5251.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.716α = 90
b = 63.245β = 90
c = 120.365γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2015-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
121590.80.0450.99918.75.12587432.39
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)
122.0590.80.3633.95.4

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 REPLACEMENTTHROUGHOUT1spv21524291125389.760.187180.184980.23134RANDOM42.243
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]
2.231.59-3.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.247
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg14.757
r_dihedral_angle_1_deg6.703
r_long_range_B_refined6.698
r_long_range_B_other6.667
r_scangle_other5.158
r_mcangle_it3.446
r_mcangle_other3.446
r_scbond_it3.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.247
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg14.757
r_dihedral_angle_1_deg6.703
r_long_range_B_refined6.698
r_long_range_B_other6.667
r_scangle_other5.158
r_mcangle_it3.446
r_mcangle_other3.446
r_scbond_it3.268
r_scbond_other3.267
r_mcbond_it2.373
r_mcbond_other2.37
r_angle_refined_deg1.424
r_angle_other_deg0.966
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2882
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing