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Crystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with 2-((5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)amino)-3-phenylpropanamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 6% PEG 10000, 100mM HEPES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.493 α = 90 b = 77.377 β = 90.76 c = 48.088 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2007-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.3 50 89 0.033 0.04 37.293 3.8 75896 75896 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 48.4 0.268 0.317 2.46 2.6 4103
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.3 34.02 2 75896 72035 3833 88.97 0.18972 0.18972 0.18896 0.1867 0.20382 0.2017 RANDOM 19.717
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] 0.03 -0.07 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 12.918 r_dihedral_angle_3_deg 11.202 r_dihedral_angle_1_deg 5.936 r_rigid_bond_restr 4.377 r_scbond_it 3.988 r_sphericity_free 3.905 r_sphericity_bonded 3.511 r_scangle_it 3.228 r_mcangle_it 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 12.918 r_dihedral_angle_3_deg 11.202 r_dihedral_angle_1_deg 5.936 r_rigid_bond_restr 4.377 r_scbond_it 3.988 r_sphericity_free 3.905 r_sphericity_bonded 3.511 r_scangle_it 3.228 r_mcangle_it 1.323 r_angle_refined_deg 1.107 r_mcbond_it 0.764 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.255 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.165 r_metal_ion_refined 0.153 r_xyhbond_nbd_refined 0.09 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2396 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 30
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling