5D6F

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CLS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6292Na Citrate, Tert-butanol
Crystal Properties
Matthews coefficientSolvent content
2.7455.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.11α = 90
b = 99.5β = 90
c = 101.35γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97895ESRFID29

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
11.5550990.07311.444.3765507
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)
11.551.5999.50.752.044.1

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 REPLACEMENTTHROUGHOUT5CLS1.555062177333098.960.148740.146830.18502RANDOM19.881
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]
0.280.25-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.899
r_dihedral_angle_4_deg18.578
r_dihedral_angle_3_deg13.486
r_long_range_B_refined7.246
r_long_range_B_other7.246
r_dihedral_angle_1_deg6.253
r_scangle_other3.937
r_scbond_it2.733
r_scbond_other2.725
r_mcangle_it2.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.899
r_dihedral_angle_4_deg18.578
r_dihedral_angle_3_deg13.486
r_long_range_B_refined7.246
r_long_range_B_other7.246
r_dihedral_angle_1_deg6.253
r_scangle_other3.937
r_scbond_it2.733
r_scbond_other2.725
r_mcangle_it2.446
r_mcangle_other2.445
r_angle_refined_deg2.19
r_mcbond_it1.717
r_mcbond_other1.696
r_angle_other_deg1.025
r_chiral_restr0.142
r_bond_refined_d0.023
r_gen_planes_refined0.012
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 Atoms504
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing