3CAN

Crystal structure of a domain of pyruvate-formate lyase-activating enzyme from Bacteroides vulgatus ATCC 8482


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729460% v/v Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.3763.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.768α = 90
b = 73.768β = 90
c = 101.358γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

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
11.83599.90.0764714.226922266542
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)
11.81.831000.74.114.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.83522665426580134399.840.1680.1630.1620.182RANDOM17.573
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]
0.290.29-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.39
r_dihedral_angle_4_deg15.011
r_dihedral_angle_3_deg12.153
r_dihedral_angle_1_deg5.088
r_scangle_it2.714
r_scbond_it1.821
r_angle_refined_deg1.144
r_mcangle_it1.079
r_mcbond_it0.851
r_angle_other_deg0.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.39
r_dihedral_angle_4_deg15.011
r_dihedral_angle_3_deg12.153
r_dihedral_angle_1_deg5.088
r_scangle_it2.714
r_scbond_it1.821
r_angle_refined_deg1.144
r_mcangle_it1.079
r_mcbond_it0.851
r_angle_other_deg0.842
r_symmetry_vdw_other0.28
r_symmetry_hbond_refined0.255
r_nbd_refined0.217
r_nbd_other0.192
r_symmetry_vdw_refined0.19
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.162
r_mcbond_other0.151
r_nbtor_other0.082
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1267
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
Cootmodel building
MLPHAREphasing
PHENIXphasing
REFMACphasing
ARP/wARPmodel building