7HGM

PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z438067480


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.627728% PEG MME 2000; 0.15 M ammonium sulfate; 0.1 M sodium acetate pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.7655

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.59α = 90
b = 42.36β = 90
c = 159.81γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2021-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.918076DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6142.3699.40.0690.0750.030.99811.96.337294
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.65991.5611.7230.7150.3845.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6140.9835308193999.110.206540.20450.24291RANDOM38.263
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]
0.57-0.16-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.42
r_long_range_B_refined9.571
r_dihedral_angle_1_deg7.973
r_mcangle_it4.835
r_dihedral_angle_2_deg4.698
r_scbond_it4.663
r_mcbond_it3.567
r_angle_refined_deg1.819
r_chiral_restr0.13
r_gen_planes_refined0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.42
r_long_range_B_refined9.571
r_dihedral_angle_1_deg7.973
r_mcangle_it4.835
r_dihedral_angle_2_deg4.698
r_scbond_it4.663
r_mcbond_it3.567
r_angle_refined_deg1.819
r_chiral_restr0.13
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms2127
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
REFMACphasing