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Crystal structure of asparagine oxygenase in complex with Fe(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.74 55.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.733 α = 90 b = 90.733 β = 90 c = 89.791 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
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 1.9 20 98.6 0.07 38.3 7.74 33610 260083 30.6
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 1.9 1.93 78.8 0.416 2.1 1331
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DRY 1.916 20 33221 32988 1033 99.29 0.232 0.17 0.169 0.197 0.2104 RANDOM 34.046
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] 0.35 0.17 0.35 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.27 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 11.267 r_dihedral_angle_1_deg 6.064 r_scangle_it 2.084 r_scbond_it 1.352 r_angle_refined_deg 1.193 r_angle_other_deg 0.897 r_mcangle_it 0.887 r_mcbond_it 0.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.27 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 11.267 r_dihedral_angle_1_deg 6.064 r_scangle_it 2.084 r_scbond_it 1.352 r_angle_refined_deg 1.193 r_angle_other_deg 0.897 r_mcangle_it 0.887 r_mcbond_it 0.811 r_symmetry_vdw_other 0.31 r_nbd_refined 0.207 r_nbd_other 0.2 r_nbtor_refined 0.166 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.102 r_mcbond_other 0.101 r_nbtor_other 0.083 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2477 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing