6RS8

X-ray crystal structure of LsAA9B (transition metals soak)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52940.1M HEPES/MOPS pH 7.5 12.5 %(v/v) MPD (racemic) 12.5 %(w/v) PEG 1000 12.5 %(w/v) PEG 3350 0.02M of each of Na-formate, NH4-acetate, Na-citrate, Na/K-tartrate, Na-oxamate.
Crystal Properties
Matthews coefficientSolvent content
2.1542.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.16α = 90
b = 72.58β = 90
c = 78.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.3499MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.584092.40.0550.99928.468.627805
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6272.40.3910.8262.84

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 REPLACEMENTTHROUGHOUT3EJA1.5839.3726400141397.450.115730.112670.17312RANDOM13.534
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]
0.20.21-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.786
r_dihedral_angle_4_deg12.79
r_sphericity_bonded12.069
r_dihedral_angle_3_deg11.464
r_dihedral_angle_1_deg7.106
r_rigid_bond_restr4.134
r_long_range_B_refined3.667
r_long_range_B_other3.667
r_scangle_other3.495
r_scbond_it3.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.786
r_dihedral_angle_4_deg12.79
r_sphericity_bonded12.069
r_dihedral_angle_3_deg11.464
r_dihedral_angle_1_deg7.106
r_rigid_bond_restr4.134
r_long_range_B_refined3.667
r_long_range_B_other3.667
r_scangle_other3.495
r_scbond_it3.112
r_scbond_other3.111
r_mcangle_other2.108
r_mcangle_it2.093
r_angle_refined_deg1.828
r_mcbond_it1.698
r_mcbond_other1.698
r_angle_other_deg1.057
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1645
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building