2VLB

Structure of unliganded arylmalonate decarboxylase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2292HANGING-DROP VAPOUR-DIFFUSION SETUP WITH 0.5 ML RESERVOIR SOLUTION AT 292 K. DROPS COMPOSED OF 1 MICROLITER OF PROTEIN AND RESERVOIR SOLUTIONS EACH. PROTEIN SOLUTION CONTAINS 7-8 MG/ML AMDASE, 20 MM TRIS-HCL PH 8 AND 0.5 MM BETA-MERCAPTO ETHANOL. RESERVOIR SOLUTION CONTAINS 1.4-1.8 M NA/K PHOSPHATE PH 5.8-6.4.
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.214α = 90
b = 100.988β = 90
c = 139.548γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.923098.90.0615.34.689247
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)
11.922.0293.70.432.22.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUTNONE1.9229.6487922132498.80.1780.1780.180.207RANDOM44.86
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]
3.59-2.23-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.561
r_dihedral_angle_4_deg19.036
r_dihedral_angle_3_deg14.31
r_scangle_it5.85
r_dihedral_angle_1_deg5.592
r_scbond_it3.955
r_mcangle_it2.229
r_mcbond_it1.587
r_angle_refined_deg1.403
r_nbtor_refined0.297
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6633
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
MLPHAREphasing
DMphasing