3CIA

Crystal structure of cold-aminopeptidase from Colwellia psychrerythraea


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529123 % w/v PEG 3350, 0.5 M NaCl, 0.1 M Bis-Tris, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8356.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.37α = 88.83
b = 87.1β = 70.68
c = 116.36γ = 88.43
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9799ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.746.793.50.20.098.572.2980533748272137.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.867.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1HS62.746.688053376497403497.290.250470.249430.27011RANDOM32.193
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]
0.12-0.080.05-0.290.150.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.032
r_dihedral_angle_4_deg18.715
r_dihedral_angle_3_deg18.562
r_dihedral_angle_1_deg6.553
r_scangle_it2.385
r_angle_refined_deg2.228
r_mcangle_it2.097
r_scbond_it1.544
r_mcbond_it1.172
r_symmetry_hbond_refined0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.032
r_dihedral_angle_4_deg18.715
r_dihedral_angle_3_deg18.562
r_dihedral_angle_1_deg6.553
r_scangle_it2.385
r_angle_refined_deg2.228
r_mcangle_it2.097
r_scbond_it1.544
r_mcbond_it1.172
r_symmetry_hbond_refined0.4
r_symmetry_vdw_refined0.359
r_nbtor_refined0.346
r_nbd_refined0.314
r_xyhbond_nbd_refined0.254
r_chiral_restr0.168
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18685
Nucleic Acid Atoms
Solvent Atoms919
Heterogen Atoms4

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction