3QBP

Crystal structure of fumarase Fum from Mycobacterium marinum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NO9pdb entry 3no9, molecule A residues 43 to 393

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289MymaA.01507.a.A1 PS00842 at 51.1 mg/mL against PACT screen condition A7, 0.2 M NaCl, 0.1 M NaOAc pH 5.0, 20% PEG 6000 soaked into PACT A7 with 25% EG as cryo-protectant, crystal tracking ID 218662a7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6253.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.88α = 90
b = 114.08β = 107.01
c = 98.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97946ALS5.0.1

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
11.855099.90.0914.514.6176835176663-322.3
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)
11.851.91000.5053.14.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 3no9, molecule A residues 43 to 3931.8550176519883499.90.1570.1550.18817.28
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]
-0.340.79-0.751.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.664
r_dihedral_angle_4_deg17.533
r_dihedral_angle_3_deg12.559
r_dihedral_angle_1_deg5.079
r_scangle_it3.357
r_scbond_it2
r_angle_refined_deg1.314
r_mcangle_it1.203
r_mcbond_it0.689
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.664
r_dihedral_angle_4_deg17.533
r_dihedral_angle_3_deg12.559
r_dihedral_angle_1_deg5.079
r_scangle_it3.357
r_scbond_it2
r_angle_refined_deg1.314
r_mcangle_it1.203
r_mcbond_it0.689
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12804
Nucleic Acid Atoms
Solvent Atoms1684
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction