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Crystal Structure of Hansenula polymorpha amine oxidase to 1.7 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A2V PDB entry 1A2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 8% PEG 8000, 0.3M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.146 α = 90 b = 223.082 β = 95.77 c = 104.248 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 2005-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 1.7 50 85.1 0.085 8.4 4.6 437335
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 1.7 1.76 35.3 0.55 2.8 18134
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 1A2V 1.7 37.96 437276 21965 84.95 0.149 0.147 0.1499 0.178 0.1801 RANDOM 22.284
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 35.9 r_dihedral_angle_4_deg 18.011 r_dihedral_angle_3_deg 13.164 r_dihedral_angle_1_deg 7.029 r_scangle_it 2.722 r_scbond_it 1.744 r_angle_refined_deg 1.33 r_mcangle_it 1.037 r_mcbond_it 0.678 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.9 r_dihedral_angle_4_deg 18.011 r_dihedral_angle_3_deg 13.164 r_dihedral_angle_1_deg 7.029 r_scangle_it 2.722 r_scbond_it 1.744 r_angle_refined_deg 1.33 r_mcangle_it 1.037 r_mcbond_it 0.678 r_nbtor_refined 0.307 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31166 Nucleic Acid Atoms Solvent Atoms 5055 Heterogen Atoms 184
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction