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Crystal structure of human diamine oxidase in space group C2221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C10 PDB entry 2c10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 298 0.1 M MES (pH 6.1), 12% w/v PEG 20,000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.771 α = 90 b = 96.954 β = 90 c = 178.06 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate OSMIC MIRRORS 2007-01-11 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210r 2008-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418 2 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.957 Australian Synchrotron MX1
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 1,2 2.106 178.06 95.2 0.111 0.111 15.7 7.4 45200 25.3
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) 1,2 2.1 2.21 96.2 0.299 0.299 2.5 3 6562
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB entry 2c10 2.11 89.09 45199 45199 2288 94.55 0.239 0.239 0.236 0.2368 0.29 0.2913 RANDOM 26.043
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] -1.95 -1.74 3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.806 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 13.578 r_dihedral_angle_1_deg 6.739 r_scangle_it 1.792 r_angle_refined_deg 1.224 r_scbond_it 1.136 r_angle_other_deg 0.82 r_mcangle_it 0.777 r_mcbond_it 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.806 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 13.578 r_dihedral_angle_1_deg 6.739 r_scangle_it 1.792 r_angle_refined_deg 1.224 r_scbond_it 1.136 r_angle_other_deg 0.82 r_mcangle_it 0.777 r_mcbond_it 0.431 r_mcbond_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5587 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 79
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing