4PX1

CRYSTAL STRUCTURE OF Maleylacetoacetate isomerase from Methylobacteriu extorquens AM1 WITH BOUND MALONATE (TARGET EFI-507068)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NIVPDB ENTRY 3NIV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298PROTEIN (10 MM TRIS, 150 MM NACL, 5% GLYCEROL, 5 MM DTT); RESERVOIR (0.1 M HEPES-NAOH, PH 7.0, 1.1M SODIUM MALONATE, 0.5% (v/v) Jeffamine ED-2001 (MCSG2 B10); CRYOPROTECTION: (RESERVOIR), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
3.0659.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.568α = 90
b = 109.568β = 90
c = 184.772γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2014-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

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
11.855099.90.1220.12227.221.85664518.181
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)
11.851.9299.90.90.93.922

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3NIV1.8529.15454646170599.70.172320.171170.21019RANDOM28.16
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]
0.510.260.51-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.652
r_dihedral_angle_4_deg18.798
r_dihedral_angle_3_deg12.489
r_long_range_B_other11.768
r_long_range_B_refined11.713
r_scangle_other9.72
r_scbond_other9.076
r_scbond_it9.071
r_mcangle_it8.635
r_mcangle_other8.633
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.652
r_dihedral_angle_4_deg18.798
r_dihedral_angle_3_deg12.489
r_long_range_B_other11.768
r_long_range_B_refined11.713
r_scangle_other9.72
r_scbond_other9.076
r_scbond_it9.071
r_mcangle_it8.635
r_mcangle_other8.633
r_mcbond_other8.278
r_mcbond_it8.275
r_dihedral_angle_1_deg5.117
r_angle_refined_deg1.199
r_angle_other_deg0.779
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3334
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms15

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling