8AXY

Staphylococcus aureus endonuclease IV orthorhombic crystal form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291- 0.1 M HEPES pH 7.0 - 2.2 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.5451.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.857α = 90
b = 82.581β = 90
c = 105.091γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.800DiamondI04

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
11.0552.54599.10.063114.27.2156665
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)
11.051.0795.81.8820.3190.56.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1xp31.0552.545156428778398.9420.1370.13580.157715.324
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]
-0.0420.795-0.754
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.184
r_dihedral_angle_4_deg16.411
r_dihedral_angle_3_deg12.21
r_dihedral_angle_1_deg6.01
r_lrange_it4.006
r_lrange_other2.993
r_scangle_it2.187
r_scangle_other1.978
r_scbond_it1.685
r_angle_refined_deg1.566
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.184
r_dihedral_angle_4_deg16.411
r_dihedral_angle_3_deg12.21
r_dihedral_angle_1_deg6.01
r_lrange_it4.006
r_lrange_other2.993
r_scangle_it2.187
r_scangle_other1.978
r_scbond_it1.685
r_angle_refined_deg1.566
r_mcangle_it1.566
r_mcangle_other1.566
r_scbond_other1.562
r_angle_other_deg1.505
r_rigid_bond_restr1.488
r_mcbond_it1.126
r_mcbond_other1.124
r_nbd_refined0.211
r_symmetry_nbd_refined0.198
r_nbd_other0.182
r_nbtor_refined0.17
r_symmetry_nbd_other0.169
r_symmetry_xyhbond_nbd_refined0.153
r_xyhbond_nbd_refined0.148
r_chiral_restr0.09
r_symmetry_nbtor_other0.085
r_xyhbond_nbd_other0.023
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2333
Nucleic Acid Atoms
Solvent Atoms521
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MoRDaphasing