6E6U

Variant C89S of Dieckmann cyclase, NcmC


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72821.7 M ammonium sulfate, 2.5% PEG 400, 0.1 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.243.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.361α = 90
b = 80.361β = 90
c = 78.323γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.5580.3699.40.08916.811.871503
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)
11.5521.5571.141

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 REPLACEMENTTHROUGHOUT6E6Y1.5580.3667900357099.40.175180.173180.21508RANDOM23.98
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]
0.410.41-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.39
r_dihedral_angle_4_deg20.231
r_dihedral_angle_3_deg12.879
r_long_range_B_refined8.421
r_long_range_B_other7.465
r_dihedral_angle_1_deg5.916
r_scangle_other5.092
r_scbond_it3.477
r_scbond_other3.461
r_mcangle_other3.241
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.39
r_dihedral_angle_4_deg20.231
r_dihedral_angle_3_deg12.879
r_long_range_B_refined8.421
r_long_range_B_other7.465
r_dihedral_angle_1_deg5.916
r_scangle_other5.092
r_scbond_it3.477
r_scbond_other3.461
r_mcangle_other3.241
r_mcangle_it3.24
r_mcbond_it2.322
r_mcbond_other2.32
r_angle_refined_deg2.084
r_angle_other_deg1.158
r_chiral_restr0.139
r_bond_refined_d0.021
r_gen_planes_refined0.012
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 Atoms3936
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing