☰ Navigation Tabs
Crystal structure of reduced murine N1-acetylpolyamine oxidase in complex with N1-acetylspermine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PROTEIN AT 23MG/ML IN 20 MM HEPES, PH 7.0, 100 MM NACL, 5% (V/V) GLYCEROL AND 2.5 MM TCEP WAS EQUILIBRATED AGAINST 2.2 M (NH4)2SO4, 0.2 M NASCN, 0.1 M TRIS PH 8. N1-ACETYL SPERMINE WAS SOAKED INTO PRE-FORMED CRYSTAL
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.99 α = 90 b = 121.99 β = 90 c = 54.91 γ = 120
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 2016-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.975 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 40.81 88.8 0.066 20.1 10.1 81328 18.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 51.5 0.417 0.908 4.5 8.4
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 5LAE 1.4 40.81 80940 4187 88.2 0.181 0.18 0.1757 0.2 0.1941 RANDOM 21.77
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] -0.2446 -0.2446 0.4892
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.5 t_omega_torsion 3.93 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.5 t_omega_torsion 3.93 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3672 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 75
Software Software Software Name Purpose BUSTER refinement Aimless data scaling XDS data reduction MOLREP phasing