2V3W

Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.704α = 90
b = 139.938β = 90
c = 169.054γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHRH-COATED SI MIRROR, RH- COATED TOROIDAL SI MIRROR2006-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-3MAX III911-3

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
12.2107.8970.128.82.9111569627.8
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)
12.22.3299.20.462.22.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BFD2.235105886561096.50.1820.180.228RANDOM21.35
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]
3.37-1.4-1.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.652
r_dihedral_angle_4_deg18.066
r_dihedral_angle_3_deg13.425
r_dihedral_angle_1_deg5.852
r_scangle_it2
r_scbond_it1.372
r_angle_refined_deg1.125
r_mcangle_it1.028
r_mcbond_it0.914
r_angle_other_deg0.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.652
r_dihedral_angle_4_deg18.066
r_dihedral_angle_3_deg13.425
r_dihedral_angle_1_deg5.852
r_scangle_it2
r_scbond_it1.372
r_angle_refined_deg1.125
r_mcangle_it1.028
r_mcbond_it0.914
r_angle_other_deg0.858
r_nbd_refined0.191
r_nbd_other0.184
r_nbtor_refined0.168
r_symmetry_vdw_other0.147
r_xyhbond_nbd_refined0.144
r_symmetry_hbond_refined0.128
r_nbtor_other0.084
r_symmetry_vdw_refined0.084
r_chiral_restr0.061
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15780
Nucleic Acid Atoms
Solvent Atoms949
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing