2HBX

Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.7529815% PEG 5000, 0.2M MgCl2, pH 8.75, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.569α = 90
b = 91.569β = 90
c = 167.91γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97945APS19-ID

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
12.55099.40.06213.17.82544742
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)
12.52.591000.4468.12505

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.550425404129399.420.1910.1890.238RANDOM69.077
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]
1.071.07-2.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.784
r_dihedral_angle_4_deg18.019
r_dihedral_angle_3_deg16.923
r_dihedral_angle_1_deg6.22
r_scangle_it2.544
r_scbond_it1.647
r_angle_refined_deg1.345
r_mcangle_it1.024
r_mcbond_it0.609
r_symmetry_hbond_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.784
r_dihedral_angle_4_deg18.019
r_dihedral_angle_3_deg16.923
r_dihedral_angle_1_deg6.22
r_scangle_it2.544
r_scbond_it1.647
r_angle_refined_deg1.345
r_mcangle_it1.024
r_mcbond_it0.609
r_symmetry_hbond_refined0.315
r_nbtor_refined0.308
r_nbd_refined0.21
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.149
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5190
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection