3B1Y

Crystal structure of an S. thermophilus NFeoB T35A mutant bound to GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LX8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.1M MIB buffer, 25%(w/v) PEG 1500, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.8α = 90
b = 42.8β = 90
c = 281.2γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102011-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95370Australian SynchrotronMX1

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
12.55099.30.07925.110.199809980
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)
12.52.5489.20.3582.33.4431

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 REPLACEMENTTHROUGHOUT3LX82.542.299797979797398.320.22440.22030.2605RANDOM35.8876
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]
0.550.55-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.706
r_dihedral_angle_4_deg14.796
r_dihedral_angle_3_deg13.402
r_dihedral_angle_1_deg4.174
r_scangle_it2.548
r_scbond_it1.51
r_angle_refined_deg1.483
r_angle_other_deg1.134
r_mcangle_it0.996
r_mcbond_it0.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.706
r_dihedral_angle_4_deg14.796
r_dihedral_angle_3_deg13.402
r_dihedral_angle_1_deg4.174
r_scangle_it2.548
r_scbond_it1.51
r_angle_refined_deg1.483
r_angle_other_deg1.134
r_mcangle_it0.996
r_mcbond_it0.522
r_mcbond_other0.084
r_chiral_restr0.065
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1963
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms28

Software

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