3IXL

Crystal structure of the Gly74Cys-Cys188Ser mutant of arylmalonate decarboxylase in the liganded form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DTVPDB ENTRY 3DTV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62931.2M ammonium sulfate, 15%(w/v) PEG 5000, 10mM alpha-bromophenylacetate, 1%(v/v) dioxan, 70mM HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0238.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.392α = 90
b = 63.353β = 90
c = 82.413γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2008-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0000SPring-8BL26B1

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
11.4510098.80.054350261
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)
1.451.4870.80.2465.14

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 3DTV1.452033171175695.890.171850.170720.19347RANDOM13.309
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]
-0.19-0.30.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.461
r_dihedral_angle_4_deg14.526
r_dihedral_angle_3_deg11.843
r_dihedral_angle_1_deg5.537
r_scangle_it2.934
r_scbond_it1.813
r_angle_refined_deg1.298
r_mcangle_it1.092
r_mcbond_it0.668
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.461
r_dihedral_angle_4_deg14.526
r_dihedral_angle_3_deg11.843
r_dihedral_angle_1_deg5.537
r_scangle_it2.934
r_scbond_it1.813
r_angle_refined_deg1.298
r_mcangle_it1.092
r_mcbond_it0.668
r_nbtor_refined0.305
r_nbd_refined0.195
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.104
r_chiral_restr0.084
r_xyhbond_nbd_refined0.084
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1703
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms21

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling