3LX5

Crystal structure of mGMPPNP-bound NFeoB from S. thermophilus


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.02M Malic acid, 0.04M MES, 0.04M Tris, 25% (w/v) PEG 1500, pH 8.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4950.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.1α = 90
b = 82.2β = 90
c = 148.8γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR 345 mm plateOsmic mirrors2009-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5412

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
11.95097.80.11814.25.72384723847-3-324.9
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)
11.91.9385.40.3363.54.41026

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT3HYR1.923.61-323665236651209980.1990.1970.241RANDOM18.057
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]
-0.872.05-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.262
r_dihedral_angle_4_deg17.891
r_dihedral_angle_3_deg12.694
r_dihedral_angle_1_deg5.184
r_scangle_it3.239
r_scbond_it2.254
r_mcangle_it2.135
r_mcbond_it1.486
r_angle_refined_deg1.479
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.262
r_dihedral_angle_4_deg17.891
r_dihedral_angle_3_deg12.694
r_dihedral_angle_1_deg5.184
r_scangle_it3.239
r_scbond_it2.254
r_mcangle_it2.135
r_mcbond_it1.486
r_angle_refined_deg1.479
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2027
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms49

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling