8RYG | pdb_00008ryg

VioH in complex with SAH from Cystobacter Violaceus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-A0A2S1TM86-F1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32931.4 M sodium potassium phosphate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.01α = 90
b = 77.6β = 90
c = 84.39γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.13091.50.0998.23.621394
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.292.70.542.83.5

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 REPLACEMENTTHROUGHOUT2.13020315106990.360.200050.197380.20970.24940.2574RANDOM24.482
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]
0.37-3.483.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.468
r_dihedral_angle_4_deg17.714
r_dihedral_angle_3_deg14.265
r_dihedral_angle_1_deg6.653
r_long_range_B_refined2.245
r_long_range_B_other2.224
r_scangle_other1.659
r_mcangle_it1.631
r_mcangle_other1.631
r_angle_refined_deg1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.468
r_dihedral_angle_4_deg17.714
r_dihedral_angle_3_deg14.265
r_dihedral_angle_1_deg6.653
r_long_range_B_refined2.245
r_long_range_B_other2.224
r_scangle_other1.659
r_mcangle_it1.631
r_mcangle_other1.631
r_angle_refined_deg1.23
r_scbond_other1.222
r_scbond_it1.221
r_mcbond_it1.137
r_mcbond_other1.137
r_angle_other_deg1.083
r_rigid_bond_restr0.512
r_chiral_restr0.047
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3722
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing