3I8X | pdb_00003i8x

Structure of the cytosolic domain of E. coli FeoB, GDP-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I8S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.928510 % PEG 4000, 100 mM Na-malonate, pH 4.9, VAPOR DIFFUSION, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.1141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.731α = 90
b = 56.058β = 91.7
c = 90.799γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-30.9085MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2525.1535991

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3I8S2.2525.143417934179179899.990.189460.186220.190.249650.25RANDOM21.955
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]
0.030.02-0.040.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.197
r_dihedral_angle_4_deg18.024
r_dihedral_angle_3_deg16.83
r_dihedral_angle_1_deg6.431
r_scangle_it3.016
r_scbond_it2.052
r_angle_refined_deg1.516
r_mcangle_it1.293
r_mcbond_it1.116
r_angle_other_deg0.963
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6045
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms84

Software

Software
Software NamePurpose
ProDCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling