5CLS

Structure of human methionine aminopeptidase-2 complexed with spiroepoxytriazole inhibitor (+)-31a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.4292Na Citrate, Tert-butanol
Crystal Properties
Matthews coefficientSolvent content
2.7455.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.62α = 90
b = 101.18β = 90
c = 100.28γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

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
11.755699.50.05316.23.5845986
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)
11.751.79599.60.75823.1

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 REPLACEMENTTHROUGHOUT1.7555.8244561142599.490.160950.160010.18885RANDOM22.373
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]
1.8-2.040.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.557
r_dihedral_angle_4_deg16.853
r_dihedral_angle_3_deg13.726
r_long_range_B_refined7.863
r_long_range_B_other7.703
r_dihedral_angle_1_deg6.924
r_scangle_other3.758
r_mcangle_it2.978
r_mcangle_other2.977
r_scbond_it2.608
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.557
r_dihedral_angle_4_deg16.853
r_dihedral_angle_3_deg13.726
r_long_range_B_refined7.863
r_long_range_B_other7.703
r_dihedral_angle_1_deg6.924
r_scangle_other3.758
r_mcangle_it2.978
r_mcangle_other2.977
r_scbond_it2.608
r_scbond_other2.572
r_angle_refined_deg2.018
r_mcbond_it1.997
r_mcbond_other1.997
r_angle_other_deg0.918
r_chiral_restr0.131
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2894
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing