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Structure of human methionine aminopeptidase 2 with covalent spiroepoxytriazole inhibitor (-)-31b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 292 Na Citrate, Tert-butanol
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.6 α = 90 b = 98.79 β = 90 c = 101.43 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.07160 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.49 50 99.3 0.053 13.94 4.33 73029
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.529 99.6 0.74 2.17 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CLS 1.49 50 69344 3685 99.27 0.11248 0.11013 0.1316 0.15559 0.1716 RANDOM 25.327
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] 1.07 -0.11 -0.96
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.835 r_dihedral_angle_2_deg 31.45 r_dihedral_angle_4_deg 16.927 r_sphericity_bonded 14.845 r_dihedral_angle_3_deg 12.561 r_long_range_B_refined 6.669 r_long_range_B_other 6.592 r_dihedral_angle_1_deg 6.047 r_scangle_other 5.771 r_rigid_bond_restr 4.927
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.835 r_dihedral_angle_2_deg 31.45 r_dihedral_angle_4_deg 16.927 r_sphericity_bonded 14.845 r_dihedral_angle_3_deg 12.561 r_long_range_B_refined 6.669 r_long_range_B_other 6.592 r_dihedral_angle_1_deg 6.047 r_scangle_other 5.771 r_rigid_bond_restr 4.927 r_scbond_it 4.844 r_scbond_other 4.843 r_mcangle_it 4.553 r_mcangle_other 4.552 r_mcbond_it 3.867 r_mcbond_other 3.848 r_angle_refined_deg 1.873 r_angle_other_deg 1.692 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2901 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing