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Structure of human methionine aminopeptidase-2 complexed with 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 5.6 292 Na Citrate, Tert-butanol
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.11 α = 90 b = 99.5 β = 90 c = 101.35 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 2015-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97895 ESRF ID29
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 1.55 50 99 0.073 11.44 4.37 65507
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 1.55 1.59 99.5 0.75 2.04 4.1
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 1.55 50 62177 3330 98.96 0.14874 0.14683 0.1704 0.18502 0.2043 RANDOM 19.881
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] 0.28 0.25 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 18.578 r_dihedral_angle_3_deg 13.486 r_long_range_B_refined 7.246 r_long_range_B_other 7.246 r_dihedral_angle_1_deg 6.253 r_scangle_other 3.937 r_scbond_it 2.733 r_scbond_other 2.725 r_mcangle_it 2.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 18.578 r_dihedral_angle_3_deg 13.486 r_long_range_B_refined 7.246 r_long_range_B_other 7.246 r_dihedral_angle_1_deg 6.253 r_scangle_other 3.937 r_scbond_it 2.733 r_scbond_other 2.725 r_mcangle_it 2.446 r_mcangle_other 2.445 r_angle_refined_deg 2.19 r_mcbond_it 1.717 r_mcbond_other 1.696 r_angle_other_deg 1.025 r_chiral_restr 0.142 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing