6BON

Crystal structure of 2-methylcitrate synthase from Aspergillus fumigatus with oxaloacetate and coenzyme-A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UQO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1 M Bis-Tris pH 6.5, 28% PEGMME2000 1.0 mM oxaloacetate 1.0 mM coenzyme-A 1.0 mM Guanosine monophosphate
Crystal Properties
Matthews coefficientSolvent content
2.0640.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.869α = 90
b = 93.235β = 90
c = 124.867γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.355096.10.0770.0770.1190.05214.54.732572-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.3999.10.5240.5240.6780.3082.354.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5UQO2.355030916163595.350.206440.203840.25564RANDOM37.116
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]
-0.722.27-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.683
r_dihedral_angle_4_deg16.984
r_dihedral_angle_3_deg14.113
r_dihedral_angle_1_deg5.017
r_long_range_B_refined4.815
r_long_range_B_other4.815
r_angle_other_deg3.641
r_mcangle_it2.971
r_mcangle_other2.971
r_scangle_other2.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.683
r_dihedral_angle_4_deg16.984
r_dihedral_angle_3_deg14.113
r_dihedral_angle_1_deg5.017
r_long_range_B_refined4.815
r_long_range_B_other4.815
r_angle_other_deg3.641
r_mcangle_it2.971
r_mcangle_other2.971
r_scangle_other2.848
r_mcbond_it1.786
r_mcbond_other1.784
r_scbond_it1.696
r_scbond_other1.695
r_angle_refined_deg1.422
r_chiral_restr0.086
r_gen_planes_other0.012
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6744
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing