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Crystal structure of aminopeptidase equipped with PAD from Aneurinibacillus sp. AM-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 5.8 293 13% PEG 6000, 0.2M Zinc acetate, 0.1M MES-NaOH, pH 5.8
Crystal Properties Matthews coefficient Solvent content 2.7 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.18 α = 90 b = 68.443 β = 90 c = 76.589 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD BRUKER SMART 6000 2012-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 40 93.4 27.6 4.8 89717
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 2EK9 1.4 39.8 85042 4444 92.93 0.18085 0.1787 0.1791 0.22284 0.2221 RANDOM 25.748
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_4_deg 16.062 r_dihedral_angle_3_deg 14.89 r_dihedral_angle_1_deg 6.224 r_scangle_it 5.919 r_scbond_it 3.568 r_mcangle_it 2.353 r_angle_refined_deg 2.268 r_mcbond_it 1.473 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_4_deg 16.062 r_dihedral_angle_3_deg 14.89 r_dihedral_angle_1_deg 6.224 r_scangle_it 5.919 r_scbond_it 3.568 r_mcangle_it 2.353 r_angle_refined_deg 2.268 r_mcbond_it 1.473 r_chiral_restr 0.153 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3119 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing