3IXM

Structure of the Gly74Cys mutant of arylmalonate decarboxylase in the sulfate ion associated 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 DROP6.22931.2M ammonium sulfate, 15%(w/v) glycerol, 0.1M HEPES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1342.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.73α = 90
b = 100.73β = 90
c = 54.165γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirror2008-04-22MSINGLE 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
11.910094.20.053160541
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)
1.91.931000.129

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 3DTV1.9201523680499.780.183110.180020.24462RANDOM23.296
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]
-0.5-0.25-0.50.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.095
r_dihedral_angle_4_deg20.903
r_dihedral_angle_3_deg16.501
r_dihedral_angle_1_deg6.347
r_scangle_it4.739
r_scbond_it2.958
r_mcangle_it1.824
r_angle_refined_deg1.718
r_mcbond_it1.097
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.095
r_dihedral_angle_4_deg20.903
r_dihedral_angle_3_deg16.501
r_dihedral_angle_1_deg6.347
r_scangle_it4.739
r_scbond_it2.958
r_mcangle_it1.824
r_angle_refined_deg1.718
r_mcbond_it1.097
r_nbtor_refined0.308
r_symmetry_hbond_refined0.289
r_symmetry_vdw_refined0.239
r_nbd_refined0.224
r_xyhbond_nbd_refined0.2
r_chiral_restr0.121
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1673
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms10

Software

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