5LW0

Oryza sativa APL macrodomain in complex with ADP-ribose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429325% PEG 1500 + 0.1 M SPG buffer (succinic acid, sodium phosphate monobasic monohydrate and glycine)
Crystal Properties
Matthews coefficientSolvent content
2.3246.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.496α = 90
b = 91.318β = 103.32
c = 62.882γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.6556.3197.40.080.99612.86.747191
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)
11.651.6877.70.4060.8753.25.2

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 REPLACEMENTTHROUGHOUT5LW61.6556.3144846234497.160.15640.154770.18727RANDOM24.533
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]
-1.370.310.140.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.801
r_dihedral_angle_4_deg19.214
r_dihedral_angle_3_deg14.553
r_long_range_B_refined7.94
r_long_range_B_other7.871
r_dihedral_angle_1_deg5.965
r_scangle_other5.939
r_scbond_it3.957
r_scbond_other3.957
r_mcangle_other3.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.801
r_dihedral_angle_4_deg19.214
r_dihedral_angle_3_deg14.553
r_long_range_B_refined7.94
r_long_range_B_other7.871
r_dihedral_angle_1_deg5.965
r_scangle_other5.939
r_scbond_it3.957
r_scbond_other3.957
r_mcangle_other3.357
r_mcangle_it3.355
r_mcbond_it2.319
r_mcbond_other2.277
r_angle_refined_deg1.564
r_angle_other_deg0.958
r_chiral_restr0.101
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms3113
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing