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Crystal structure of human methionine aminopeptidase-2 complexed with (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methyl-2-buten-1-yl)-2-oxiranyl]-1-oxaspiro[2.5]oct-6-yl N-(trans-4-aminocyclohexyl)carbamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D6F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.88 57.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.05 α = 90 b = 101.127 β = 98.755 c = 83.737 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2022-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.73 44.84 99.6 0.089 0.105 0.055 0.998 12.5 6.9 101909
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 92.3 1.288 0.866 0.649 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.731 44.84 101840 5131 99.836 0.183 0.1811 0.1816 0.215 0.2162 28.255
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] 2.949 0.841 -1.827 -1.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.512 r_dihedral_angle_6_deg 17.142 r_dihedral_angle_3_deg 14.94 r_lrange_it 7.442 r_lrange_other 7.373 r_dihedral_angle_1_deg 7.169 r_dihedral_angle_other_2_deg 6.07 r_scangle_it 6.048 r_scangle_other 6.048 r_mcangle_it 4.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.512 r_dihedral_angle_6_deg 17.142 r_dihedral_angle_3_deg 14.94 r_lrange_it 7.442 r_lrange_other 7.373 r_dihedral_angle_1_deg 7.169 r_dihedral_angle_other_2_deg 6.07 r_scangle_it 6.048 r_scangle_other 6.048 r_mcangle_it 4.488 r_mcangle_other 4.488 r_scbond_it 4.459 r_scbond_other 4.458 r_mcbond_it 3.558 r_mcbond_other 3.558 r_angle_refined_deg 2.13 r_angle_other_deg 0.739 r_nbd_other 0.238 r_nbd_refined 0.222 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.182 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.147 r_chiral_restr 0.132 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.034 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5779 Nucleic Acid Atoms Solvent Atoms 568 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing