2IG9

Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in a new spacegroup.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F1XPDB entry 1F1X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529218% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, and then 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2945.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.445α = 90
b = 152.802β = 90
c = 99.714γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12005-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.23983ALS4.2.2

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
11.953.1599.80.0997.13.18133141132886
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)
11.91.9799.90.53223.113150

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 1F1X1.946.08132683132683668099.670.189760.18740.23443RANDOM23.337
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.881
r_dihedral_angle_4_deg17.693
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg7.036
r_scangle_it3.065
r_scbond_it2.084
r_angle_refined_deg1.455
r_mcangle_it1.166
r_mcbond_it0.956
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.881
r_dihedral_angle_4_deg17.693
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg7.036
r_scangle_it3.065
r_scbond_it2.084
r_angle_refined_deg1.455
r_mcangle_it1.166
r_mcbond_it0.956
r_nbtor_refined0.305
r_symmetry_hbond_refined0.223
r_nbd_refined0.201
r_symmetry_vdw_refined0.189
r_symmetry_metal_ion_refined0.165
r_xyhbond_nbd_refined0.148
r_metal_ion_refined0.105
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11600
Nucleic Acid Atoms
Solvent Atoms1248
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing