3B1V

Crystal structure of an S. thermophilus NFeoB E67A mutant bound to mGMPPNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LX5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.2M NaCl, 0.1M HEPES, 20%(w/v) PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5551.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.2α = 90
b = 82.7β = 90
c = 150.9γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95369Australian SynchrotronMX2

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
11.855097.20.07215.34.12603726037
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)
11.851.8896.30.7621.94.11257

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3LX51.8541.352591024598131296.270.186650.184870.22257RANDOM37.114
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]
-0.990.580.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_4_deg17.241
r_dihedral_angle_3_deg11.609
r_dihedral_angle_1_deg4.931
r_scangle_it4.068
r_scbond_it2.467
r_mcangle_it1.607
r_angle_refined_deg1.431
r_angle_other_deg0.922
r_mcbond_it0.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_4_deg17.241
r_dihedral_angle_3_deg11.609
r_dihedral_angle_1_deg4.931
r_scangle_it4.068
r_scbond_it2.467
r_mcangle_it1.607
r_angle_refined_deg1.431
r_angle_other_deg0.922
r_mcbond_it0.909
r_mcbond_other0.237
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2027
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms44

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing