3BMZ | pdb_00003bmz

Violacein biosynthetic enzyme VioE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529825% (v/v) PEG-400, 20% (w/v) PEG-3350, 0.1 M magnesium chloride, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1943.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.527α = 90
b = 82.477β = 90
c = 90.633γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray141.6CCDADSC QUANTUM 3152007-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9795APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.215090.60.06635.713.9111465111465
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.211.2554.30.2583.43.26598

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.2145.31105792560590.590.169120.167810.170.194590.2RANDOM12.818
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]
0.040.19-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.465
r_dihedral_angle_4_deg15.689
r_dihedral_angle_3_deg11.194
r_dihedral_angle_1_deg5.86
r_sphericity_bonded2.654
r_sphericity_free2.541
r_scangle_it2.394
r_scbond_it1.827
r_rigid_bond_restr1.728
r_mcangle_it1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.465
r_dihedral_angle_4_deg15.689
r_dihedral_angle_3_deg11.194
r_dihedral_angle_1_deg5.86
r_sphericity_bonded2.654
r_sphericity_free2.541
r_scangle_it2.394
r_scbond_it1.827
r_rigid_bond_restr1.728
r_mcangle_it1.35
r_angle_refined_deg1.209
r_mcbond_it1.157
r_angle_other_deg0.816
r_mcbond_other0.403
r_symmetry_vdw_other0.272
r_nbd_other0.196
r_nbd_refined0.18
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.106
r_symmetry_hbond_refined0.088
r_nbtor_other0.08
r_chiral_restr0.077
r_symmetry_vdw_refined0.035
r_bond_refined_d0.006
r_gen_planes_refined0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2984
Nucleic Acid Atoms
Solvent Atoms605
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing