4E0F

Crystallographic structure of trimeric Riboflavin Synthase from Brucella abortus in complex with riboflavin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I8DMonomer from PDB entry 1I8D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429212% PEG 8000, 10% Glycerol, 0.5M Potassium Chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2745.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.98α = 90
b = 91.82β = 90
c = 98.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 270Toroidal focusing mirror2011-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1.0000NSLSX6A

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
12.8567.2598.70.1230.1235.98.6151671516747.8
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)
12.85398.60.3850.3851.98.72177

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMonomer from PDB entry 1I8D2.8567.25143751437575198.060.218120.218120.215650.26705RANDOM22.521
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]
-0.370.82-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.537
r_dihedral_angle_3_deg17.271
r_dihedral_angle_4_deg12.902
r_dihedral_angle_1_deg4.46
r_angle_refined_deg0.937
r_scangle_it0.88
r_scbond_it0.481
r_mcangle_it0.426
r_mcbond_it0.225
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.537
r_dihedral_angle_3_deg17.271
r_dihedral_angle_4_deg12.902
r_dihedral_angle_1_deg4.46
r_angle_refined_deg0.937
r_scangle_it0.88
r_scbond_it0.481
r_mcangle_it0.426
r_mcbond_it0.225
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4590
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms27

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling