3DTV

Crystal structure of arylmalonate decarboxylase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
182931.5M ammonium sulfate, 12%(W/V) glycerol, 0.1M Tris-HCl pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.63α = 90
b = 99.321β = 90
c = 140.263γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210TOROIDAL MIRROR2007-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B2SPring-8BL44B2

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
12.15099.70.04832.47.2682791
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)
12.12.1498.20.3274.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRTHROUGHOUT2.12064363338699.70.1950.1930.241RANDOM47.03
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]
1.63-0.36-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.24
r_dihedral_angle_4_deg21.876
r_dihedral_angle_3_deg18.658
r_dihedral_angle_1_deg6.77
r_scangle_it4.856
r_mcangle_it4.176
r_scbond_it3.644
r_mcbond_it2.961
r_angle_refined_deg1.553
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.24
r_dihedral_angle_4_deg21.876
r_dihedral_angle_3_deg18.658
r_dihedral_angle_1_deg6.77
r_scangle_it4.856
r_mcangle_it4.176
r_scbond_it3.644
r_mcbond_it2.961
r_angle_refined_deg1.553
r_nbtor_refined0.315
r_nbd_refined0.235
r_symmetry_hbond_refined0.228
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.17
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms6628
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms78

Software

Software
Software NamePurpose
DMmodel building
MLPHAREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling