5N0W

Crystal structure of OphA-DeltaC6 mutant R72A 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
3.5965.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.098α = 90
b = 92.276β = 90
c = 85.684γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
11.9349.898.70.0710.99617.44.496972
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)
11.932.0297.50.5680.7681.33.8

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 REPLACEMENTTHROUGHOUT5N0O1.9349.891990491198.650.194760.193630.21609RANDOM45.126
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]
1.51-0.48-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.527
r_dihedral_angle_4_deg15.894
r_dihedral_angle_3_deg12.486
r_long_range_B_refined5.814
r_dihedral_angle_1_deg5.782
r_long_range_B_other5.583
r_mcangle_it2.167
r_mcangle_other2.166
r_scangle_other2.12
r_angle_refined_deg1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.527
r_dihedral_angle_4_deg15.894
r_dihedral_angle_3_deg12.486
r_long_range_B_refined5.814
r_dihedral_angle_1_deg5.782
r_long_range_B_other5.583
r_mcangle_it2.167
r_mcangle_other2.166
r_scangle_other2.12
r_angle_refined_deg1.38
r_mcbond_it1.24
r_mcbond_other1.24
r_scbond_it1.231
r_scbond_other1.231
r_angle_other_deg0.922
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms6071
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms60

Software

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