8PMU

Crystal structure of the HC7 apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldWe used the alphafold model generated by the AlphaFold2 server.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Lithium chloride Tris PEG 8000

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.854α = 90
b = 93.854β = 90
c = 87.287γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9793ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7593.8591.90.03411.58.736731
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)
11.751.841.2090.644

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 REPLACEMENTTHROUGHOUT1.7566.3635169142391.730.192930.191310.23117RANDOM30.438
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]
0.190.19-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.772
r_dihedral_angle_3_deg14.483
r_dihedral_angle_4_deg10.549
r_long_range_B_refined7.546
r_long_range_B_other7.541
r_dihedral_angle_1_deg7.143
r_scangle_other5.734
r_scbond_it3.766
r_scbond_other3.766
r_mcangle_other3.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.772
r_dihedral_angle_3_deg14.483
r_dihedral_angle_4_deg10.549
r_long_range_B_refined7.546
r_long_range_B_other7.541
r_dihedral_angle_1_deg7.143
r_scangle_other5.734
r_scbond_it3.766
r_scbond_other3.766
r_mcangle_other3.46
r_mcangle_it3.457
r_mcbond_it2.536
r_mcbond_other2.523
r_angle_refined_deg1.932
r_angle_other_deg1.099
r_chiral_restr0.164
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2730
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing