3IAF

Structure of benzaldehyde lyase A28S mutant with monomethyl benzoylphosphonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AG0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9298100 mM MES (pH 6.9), 50% v/v PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7354.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.962α = 90
b = 150.962β = 90
c = 195.56γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2006-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97934APS23-ID-D

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
12.75097.50.1227.910.1708346906322
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)
2.72.879.40.7311.335.2

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 REPLACEMENTTHROUGHOUT2AG02.847.897083457155639499.440.217440.212580.26038RANDOM76.129
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]
0.160.080.16-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.348
r_dihedral_angle_3_deg17.296
r_dihedral_angle_4_deg15.76
r_dihedral_angle_1_deg5.254
r_mcangle_it2.338
r_scangle_it1.782
r_mcbond_it1.289
r_angle_refined_deg1.097
r_scbond_it0.988
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.348
r_dihedral_angle_3_deg17.296
r_dihedral_angle_4_deg15.76
r_dihedral_angle_1_deg5.254
r_mcangle_it2.338
r_scangle_it1.782
r_mcbond_it1.289
r_angle_refined_deg1.097
r_scbond_it0.988
r_nbtor_refined0.297
r_symmetry_vdw_refined0.261
r_nbd_refined0.199
r_xyhbond_nbd_refined0.127
r_chiral_restr0.071
r_symmetry_hbond_refined0.071
r_metal_ion_refined0.066
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16336
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms108

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
locallydata collection