3RBL

Crystal structure of Human aromatic L-amino acid decarboxylase (AADC) in the apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RBF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1vapor diffusion followed by soaking7294crystals obtained from holoAADC in 0.1 M HEPES pH 7.0, 28-30% Jeffamine ED 2001 pH 7.0 were transferred in a ML droplet to yield apoAADC, vapor diffusion followed by soaking, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.856.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.64α = 90
b = 179.64β = 90
c = 74.95γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-11-20MSINGLE WAVELENGTH
21
31
41
51
61
71
81
91
101
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
13.24127.02599.80.13113.86.42009820098
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.243.411000.4020.4021.96.22886

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3rbf3.24302012019980101999.390.2390.2390.23610.2943RANDOM46.6904
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]
1.871.87-3.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_3_deg19.478
r_dihedral_angle_4_deg18.835
r_dihedral_angle_1_deg5.961
r_scangle_it2.396
r_scbond_it1.353
r_angle_refined_deg1.271
r_mcangle_it0.919
r_mcbond_it0.464
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_3_deg19.478
r_dihedral_angle_4_deg18.835
r_dihedral_angle_1_deg5.961
r_scangle_it2.396
r_scbond_it1.353
r_angle_refined_deg1.271
r_mcangle_it0.919
r_mcbond_it0.464
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6949
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms1

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
EDNAdata collection