5OM9

Crystal structure of the human CARBOXYPEPTIDASE A1 in complex with a thiirane mechanism-based inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V77 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27720% PEG 6000, 0.2M MGCL2, 0.1 M TRIS- HCL BUFFER PH 8.0
Crystal Properties
Matthews coefficientSolvent content
238.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.901α = 90
b = 52.544β = 94.84
c = 133.984γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979490ALBAXALOC

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
11.7744.594.10.07113.169096
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)
11.771.86660.134.22.2

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 REPLACEMENTTHROUGHOUT2V771.843.6863800339096.480.157320.154450.21178RANDOM16.127
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]
-0.31-0.240.57-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.369
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg15.406
r_dihedral_angle_1_deg6.454
r_scangle_it6.174
r_scbond_it4.415
r_mcangle_it2.765
r_rigid_bond_restr2.437
r_angle_refined_deg1.852
r_mcbond_it1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.369
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg15.406
r_dihedral_angle_1_deg6.454
r_scangle_it6.174
r_scbond_it4.415
r_mcangle_it2.765
r_rigid_bond_restr2.437
r_angle_refined_deg1.852
r_mcbond_it1.83
r_chiral_restr0.148
r_bond_refined_d0.022
r_gen_planes_refined0.01
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 Atoms6283
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing