5AQ0

The structure of the Transthyretin-like domain of the first catalytic domain of the HUMAN Carboxypeptidase D


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.2244.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.773α = 90
b = 46.051β = 90.18
c = 42.73γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
10.9542.7395.50.0313.72.5928832
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)
10.95181.30.461.72

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT0.9542.7388253461095.470.153920.152820.17514RANDOM13.807
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]
0.070.51-0.140.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.183
r_dihedral_angle_4_deg20.856
r_dihedral_angle_3_deg13.376
r_scangle_it6.93
r_dihedral_angle_1_deg6.376
r_scbond_it4.86
r_mcangle_it3.216
r_rigid_bond_restr2.599
r_angle_refined_deg2.364
r_mcbond_it2.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.183
r_dihedral_angle_4_deg20.856
r_dihedral_angle_3_deg13.376
r_scangle_it6.93
r_dihedral_angle_1_deg6.376
r_scbond_it4.86
r_mcangle_it3.216
r_rigid_bond_restr2.599
r_angle_refined_deg2.364
r_mcbond_it2.198
r_chiral_restr0.419
r_bond_refined_d0.029
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1224
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
CCP4Idata scaling
MOLREPphasing