8XXC | pdb_00008xxc

DaCS-intermediate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldA0A7C6A739 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289.150.1M HEPES pH7.5, 40% v/v Polyethylene glycol 400
Crystal Properties
Matthews coefficientSolvent content
2.550.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 361.422α = 90
b = 361.422β = 90
c = 77.741γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2021-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979SSRFBL18U1

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
12.0295099.10.1850.1990.0720.98914.57.3242593
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)
12.0292.070.9830.68

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0325.072238791184996.20.1980.1960.20410.2390.2456RANDOM33.22
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]
-0.04-0.02-0.040.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.907
r_long_range_B_refined9.892
r_dihedral_angle_2_deg9.817
r_long_range_B_other9.724
r_dihedral_angle_1_deg6.88
r_scangle_other4.453
r_mcangle_it4.156
r_mcangle_other4.156
r_scbond_it2.852
r_scbond_other2.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.907
r_long_range_B_refined9.892
r_dihedral_angle_2_deg9.817
r_long_range_B_other9.724
r_dihedral_angle_1_deg6.88
r_scangle_other4.453
r_mcangle_it4.156
r_mcangle_other4.156
r_scbond_it2.852
r_scbond_other2.852
r_mcbond_it2.775
r_mcbond_other2.775
r_angle_refined_deg1.428
r_angle_other_deg0.48
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms27401
Nucleic Acid Atoms
Solvent Atoms2026
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing