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The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KSI PDB ENTRY 1KSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 288 THE PROTEIN WAS CRYSTALLISED IN 0.1 M KBR, 0.1 M ACETATE PH 5, 38% PEG1000 AT 288 K.
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.236 α = 90 b = 130.236 β = 90 c = 221.529 γ = 90
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 CCD 2004-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.5 51.6 100 0.1 13.8 5.2 126698 3.2 48
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 2.5 2.64 99.8 0.44 3.2 3.8
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 PDB ENTRY 1KSI 2.5 20 124418 6243 98.2 0.204 0.204 0.2043 0.252 0.2061 RANDOM 37.62
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] 1.83 1.83 -3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.469 r_dihedral_angle_4_deg 19.747 r_dihedral_angle_3_deg 16.582 r_dihedral_angle_1_deg 6.42 r_scangle_it 2.278 r_scbond_it 1.343 r_angle_refined_deg 1.34 r_mcangle_it 0.922 r_mcbond_it 0.517 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.469 r_dihedral_angle_4_deg 19.747 r_dihedral_angle_3_deg 16.582 r_dihedral_angle_1_deg 6.42 r_scangle_it 2.278 r_scbond_it 1.343 r_angle_refined_deg 1.34 r_mcangle_it 0.922 r_mcbond_it 0.517 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.249 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 22300 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 607
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing