3P7I

Crystal structure of Escherichia coli PhnD in complex with 2-aminoethyl phosphonate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6298.150.2M ammonium sulfate, sodium acetate trihydrate, pH 4.6, 25% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K
Crystal Properties
Matthews coefficientSolvent content
2.3948.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.094α = 90
b = 82.44β = 90
c = 54.667γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
11.7145.699.63586435721

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7145.63586435721188099.60.226970.226970.225680.25144RANDOM25.239
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]
-0.040.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.228
r_dihedral_angle_4_deg18.994
r_dihedral_angle_3_deg16.728
r_dihedral_angle_1_deg5.956
r_scangle_it5.051
r_scbond_it3.215
r_mcangle_it2.077
r_angle_refined_deg2.021
r_mcbond_it1.319
r_chiral_restr0.151
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.228
r_dihedral_angle_4_deg18.994
r_dihedral_angle_3_deg16.728
r_dihedral_angle_1_deg5.956
r_scangle_it5.051
r_scbond_it3.215
r_mcangle_it2.077
r_angle_refined_deg2.021
r_mcbond_it1.319
r_chiral_restr0.151
r_bond_refined_d0.026
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2353
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms25

Software

Software
Software NamePurpose
SPECdata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling