7CF6

Crystal structure of Beta-aspartyl dipeptidase from thermophilic keratin degrading Fervidobacterium islandicum AW-1 in complex with beta-Asp-Leu dipeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CDH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2932% Tacismate pH 5.0, 0.1 M Sodium citrate pH 5.6, 16 % w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.6253.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.609α = 90
b = 150.425β = 90
c = 151.996γ = 90
Symmetry
Space GroupP 2 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702017-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.98461PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.75099.70.310.3270.12.51046521
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7599.41.5521.6740.6130.3686.9

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 REPLACEMENTTHROUGHOUT7CDH2.7547.6634968199477.510.20020.19580.2783RANDOM46.931
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]
0.020.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.65
r_dihedral_angle_4_deg19.666
r_dihedral_angle_3_deg18.653
r_dihedral_angle_1_deg7.766
r_angle_refined_deg1.613
r_angle_other_deg1.179
r_chiral_restr0.061
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.65
r_dihedral_angle_4_deg19.666
r_dihedral_angle_3_deg18.653
r_dihedral_angle_1_deg7.766
r_angle_refined_deg1.613
r_angle_other_deg1.179
r_chiral_restr0.061
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11521
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms156

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing