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Crystal structure of asparagine oxygenase (AsnO)
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 2.82 60.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.61 α = 90 b = 91.61 β = 90 c = 90.878 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 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 1.45 23 99.7 0.06 12.6 3.85 78000 0.9 21
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 1.45 1.53 99.7 0.992 0.9 3.99 11338
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 1DRY 1.45 22.91 77685 2342 99.64 0.171 0.17 0.1795 0.186 0.1972 RANDOM 18.473
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] 0.21 0.1 0.21 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.837 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 10.898 r_dihedral_angle_1_deg 5.415 r_scangle_it 2.675 r_scbond_it 1.742 r_angle_refined_deg 1.175 r_mcangle_it 0.954 r_angle_other_deg 0.9 r_mcbond_it 0.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.837 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 10.898 r_dihedral_angle_1_deg 5.415 r_scangle_it 2.675 r_scbond_it 1.742 r_angle_refined_deg 1.175 r_mcangle_it 0.954 r_angle_other_deg 0.9 r_mcbond_it 0.856 r_symmetry_vdw_other 0.346 r_symmetry_hbond_refined 0.213 r_nbd_refined 0.211 r_nbd_other 0.206 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_refined 0.136 r_mcbond_other 0.128 r_nbtor_other 0.083 r_chiral_restr 0.065 r_metal_ion_refined 0.034 r_bond_refined_d 0.007 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 2418 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing