4QNV

Crystal structure of Cx-SAM bound CmoB from E. coli in P6122


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1M HEPES:NaOH pH 7.5, 0.2M MgCl2, 30% (v/v) PEG400, 10mM TCEP:HCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8456.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.134α = 90
b = 82.134β = 90
c = 432.516γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
12.645099.20.14415.58.52696326722
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)
12.642.691000.99348.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.6443.0825243133799.050.220860.218360.26947RANDOM48.595
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]
0.20.20.2-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.045
r_dihedral_angle_4_deg22.473
r_dihedral_angle_3_deg17.949
r_long_range_B_refined9.238
r_long_range_B_other9.238
r_dihedral_angle_1_deg7.433
r_scangle_other7.126
r_mcangle_it6.731
r_mcangle_other6.73
r_scbond_it4.936
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.045
r_dihedral_angle_4_deg22.473
r_dihedral_angle_3_deg17.949
r_long_range_B_refined9.238
r_long_range_B_other9.238
r_dihedral_angle_1_deg7.433
r_scangle_other7.126
r_mcangle_it6.731
r_mcangle_other6.73
r_scbond_it4.936
r_scbond_other4.936
r_mcbond_it4.678
r_mcbond_other4.678
r_angle_refined_deg1.536
r_angle_other_deg0.925
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.004
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 Atoms5185
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms70

Software

Software
Software NamePurpose
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling