5N0R

Crystal structure of OphA-DeltaC6 mutant Y66F in complex with SAM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5N0O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2890.3-0.4 M KSCN, 1.5-1.9 M sodium malonate and 0.1 M bicine pH 9.0
Crystal Properties
Matthews coefficientSolvent content
3.7266.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.652α = 90
b = 93.355β = 90
c = 165.355γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9281DiamondI04-1

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
11.6182.68980.025127.65.584772
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)
11.611.64980.6090.842

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5N0O1.6182.68805254197980.17830.17760.19124RANDOM38.849
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]
-0.54-0.511.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.566
r_dihedral_angle_4_deg14.767
r_dihedral_angle_3_deg11.891
r_dihedral_angle_1_deg5.591
r_long_range_B_refined4.535
r_long_range_B_other4.297
r_scangle_other1.793
r_mcangle_it1.761
r_mcangle_other1.761
r_angle_refined_deg1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.566
r_dihedral_angle_4_deg14.767
r_dihedral_angle_3_deg11.891
r_dihedral_angle_1_deg5.591
r_long_range_B_refined4.535
r_long_range_B_other4.297
r_scangle_other1.793
r_mcangle_it1.761
r_mcangle_other1.761
r_angle_refined_deg1.34
r_scbond_it1.098
r_scbond_other1.098
r_mcbond_it1.001
r_mcbond_other1.001
r_angle_other_deg0.913
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3004
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing