5LS7

Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CRY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291200 mM KSCN, 100 mM Bis-Tris propane pH 6.5, 20% v/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4650.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.863α = 90
b = 85.863β = 90
c = 80.055γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.1629.2899.60.07795.199822
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)
11.161.1893.70.3952.14.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4CRY1.1629.2894485496699.60.114580.113410.13688RANDOM17.859
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]
0.810.81-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.77
r_sphericity_free29.073
r_dihedral_angle_4_deg16.179
r_sphericity_bonded15.712
r_dihedral_angle_3_deg12.038
r_rigid_bond_restr9.893
r_dihedral_angle_1_deg5.923
r_long_range_B_refined5.47
r_long_range_B_other5.469
r_scangle_other4.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.77
r_sphericity_free29.073
r_dihedral_angle_4_deg16.179
r_sphericity_bonded15.712
r_dihedral_angle_3_deg12.038
r_rigid_bond_restr9.893
r_dihedral_angle_1_deg5.923
r_long_range_B_refined5.47
r_long_range_B_other5.469
r_scangle_other4.878
r_scbond_it3.729
r_scbond_other3.692
r_mcangle_other3.11
r_mcangle_it3.109
r_angle_refined_deg2.851
r_mcbond_it2.363
r_mcbond_other2.352
r_angle_other_deg1.21
r_chiral_restr0.164
r_bond_refined_d0.034
r_gen_planes_refined0.013
r_gen_planes_other0.004
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1993
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing