4PXO

Crystal structure of Maleylacetoacetate isomerase from Methylobacteriu extorquens AM1 WITH BOUND MALONATE AND GSH (TARGET EFI-507068)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PX1PDB ENTRY 4PX1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5PROTEIN (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), 10 MM GSH; CRYOPROTECTION: (RESERVOIR), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
3.0860.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.628α = 90
b = 109.628β = 90
c = 185.367γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2014-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85099.70.10123.414.461218-521.628
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.83100214.3

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 4PX11.85059371182499.690.145060.144180.17421RANDOM31.344
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]
0.680.340.68-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.855
r_dihedral_angle_4_deg18.984
r_dihedral_angle_3_deg12.062
r_long_range_B_other9.118
r_long_range_B_refined9.116
r_scangle_other6.835
r_scbond_it6.09
r_scbond_other6.086
r_dihedral_angle_1_deg4.962
r_mcangle_other4.442
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.855
r_dihedral_angle_4_deg18.984
r_dihedral_angle_3_deg12.062
r_long_range_B_other9.118
r_long_range_B_refined9.116
r_scangle_other6.835
r_scbond_it6.09
r_scbond_other6.086
r_dihedral_angle_1_deg4.962
r_mcangle_other4.442
r_mcangle_it4.359
r_mcbond_it4.031
r_mcbond_other3.833
r_angle_refined_deg1.195
r_angle_other_deg0.783
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms3324
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms86

Software

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