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Cystal structure of asparagine oxygenase in complex with Fe(II), 2S,3S-3-hydroxyasparagine and succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DRY PDB Entry 1DRY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 2.5 M sodium acetate, 0.1 M Hepes, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.81 56.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.308 α = 90 b = 91.308 β = 90 c = 90.867 γ = 120
Symmetry Space Group P 31 2 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 MAR CCD 165 mm 2006-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8080 EMBL/DESY, HAMBURG X13
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 1.65 23 99.4 0.052 15.1 3.69 51815 191425 24.9
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 1.65 1.74 98.4 0.539 1.7 3.49 7385
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 (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 1DRY 1.66 22.91 51776 1582 99.37 0.18371 0.1681 0.168 0.183 0.184 0.2001 RANDOM 23.14
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] 0.54 0.27 0.54 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 17.864 r_dihedral_angle_3_deg 11.37 r_dihedral_angle_1_deg 8.557 r_scangle_it 2.408 r_scbond_it 1.574 r_angle_refined_deg 1.178 r_angle_other_deg 0.871 r_mcangle_it 0.845 r_mcbond_it 0.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 17.864 r_dihedral_angle_3_deg 11.37 r_dihedral_angle_1_deg 8.557 r_scangle_it 2.408 r_scbond_it 1.574 r_angle_refined_deg 1.178 r_angle_other_deg 0.871 r_mcangle_it 0.845 r_mcbond_it 0.775 r_symmetry_vdw_other 0.338 r_nbd_refined 0.211 r_nbd_other 0.208 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.129 r_mcbond_other 0.127 r_nbtor_other 0.083 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2448 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing