4GP9

Crystal Structure of Benzoylformate Decarboxylase Mutant L403F


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BFD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3246.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.245α = 90
b = 95.55β = 90
c = 137.355γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03APS23-ID-B

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
11.075093.20.06313.87.6217292
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)
11.071.1157.60.5722.913317

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1BFD1.0745.9781.342172231084093.160.13790.13730.1503RANDOM12.628
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]
2.6708-1.4524-1.2184
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.489
f_angle_d1.602
f_chiral_restr0.095
f_bond_d0.013
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3944
Nucleic Acid Atoms
Solvent Atoms609
Heterogen Atoms42

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
DENZOdata reduction
PHENIXphasing