3BZN

Crystal Structure of Open form of Menaquinone-Specific Isochorismate Synthase, MenF


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop vapor diffusion6.5298well solution: 0.1M Bis-Tris pH 6.5, 20% PEG-MME 5000. protein solution: 50mM Tris pH 7.8, 50 mM magnesium sulfate. Drops were equal volumes well and protein., sitting drop vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.28α = 90
b = 70.49β = 90
c = 90.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105IMAGE PLATERIGAKU RAXIS IV++2004-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.9929.6299.20.0749.22.9728882
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)
1.992.0795.70.3223.22.822745

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT22028501145799.060.2060.2020.284RANDOM28.943
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]
-1.57-0.652.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.979
r_dihedral_angle_4_deg22.582
r_dihedral_angle_3_deg20.863
r_dihedral_angle_1_deg7.444
r_scangle_it4.242
r_scbond_it2.975
r_angle_refined_deg2.023
r_mcangle_it1.746
r_mcbond_it1.091
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.979
r_dihedral_angle_4_deg22.582
r_dihedral_angle_3_deg20.863
r_dihedral_angle_1_deg7.444
r_scangle_it4.242
r_scbond_it2.975
r_angle_refined_deg2.023
r_mcangle_it1.746
r_mcbond_it1.091
r_nbtor_refined0.309
r_symmetry_hbond_refined0.297
r_symmetry_vdw_refined0.245
r_nbd_refined0.225
r_xyhbond_nbd_refined0.192
r_chiral_restr0.154
r_bond_refined_d0.021
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3482
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms16

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction