2PHD

Crystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D40PDB ENTRY 2D40

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.627712% w/v EtOH, 4% w/v PEG400, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5651.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.016α = 90
b = 133.016β = 90
c = 190.748γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2005-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8423EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.9109.109990.1540.1544.34.83810338103
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.93.0699.60.470.471.64.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2D402.9203788335989189498.460.196560.193130.26239RANDOM42.108
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]
-0.84-0.841.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.922
r_dihedral_angle_4_deg22.548
r_dihedral_angle_3_deg21.232
r_dihedral_angle_1_deg7.441
r_scangle_it2.257
r_angle_refined_deg1.714
r_scbond_it1.4
r_mcangle_it1.079
r_mcbond_it0.609
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.922
r_dihedral_angle_4_deg22.548
r_dihedral_angle_3_deg21.232
r_dihedral_angle_1_deg7.441
r_scangle_it2.257
r_angle_refined_deg1.714
r_scbond_it1.4
r_mcangle_it1.079
r_mcbond_it0.609
r_nbtor_refined0.32
r_symmetry_vdw_refined0.269
r_symmetry_hbond_refined0.267
r_nbd_refined0.245
r_xyhbond_nbd_refined0.177
r_chiral_restr0.114
r_metal_ion_refined0.103
r_bond_refined_d0.016
r_gen_planes_refined0.005
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 Atoms10842
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms16

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction