2I3C

Crystal Structure of an Aspartoacylase from Homo Sapiens


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GU2PDB entry 2gu2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 M Tris PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.344 M K2HPO4, 0.056 M NaH2PO4) CRYOPROTECTED WITH WELL SOLUTION WITH 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.867.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.551α = 90
b = 145.551β = 90
c = 103.396γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2006-08-05MSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97926APS22-ID
2

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
12.848.71697.90.16410.61213.327367
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)
2.82.981.40.5821.8666.22207

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 2gu22.848.71627305137497.7940.1970.1970.1950.243RANDOM47.682
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]
0.5670.567-1.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.426
r_dihedral_angle_4_deg22.202
r_dihedral_angle_3_deg18.843
r_dihedral_angle_1_deg6.237
r_scangle_it6.166
r_scbond_it4.441
r_mcangle_it2.415
r_angle_refined_deg1.551
r_mcbond_it1.399
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.426
r_dihedral_angle_4_deg22.202
r_dihedral_angle_3_deg18.843
r_dihedral_angle_1_deg6.237
r_scangle_it6.166
r_scbond_it4.441
r_mcangle_it2.415
r_angle_refined_deg1.551
r_mcbond_it1.399
r_nbtor_refined0.321
r_nbd_refined0.229
r_metal_ion_refined0.214
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.123
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4860
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms42

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction