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Crystal structure of a putative quercetin 2,3-dioxygenase (yxag, bsu39980) from bacillus subtilis at 2.60 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y3T pdb entry 1y3tA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 277 10.0% PEG-3350, 0.4M Ammonium Tartrate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.31 76.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.416 α = 90 b = 128.659 β = 90 c = 133.889 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 2005-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.6 29.778 99.8 0.104 0.104 6.8 5.4 52320 59.22
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 2.6 2.67 100 0.771 0.771 1 4.9
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 1y3tA 2.6 29.78 52271 2666 99.64 0.169 0.167 0.1776 0.204 0.2042 RANDOM 41.565
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] 5.86 -3.68 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.217 r_dihedral_angle_4_deg 15.409 r_dihedral_angle_3_deg 13.623 r_scangle_it 6.309 r_dihedral_angle_1_deg 6.17 r_scbond_it 4.545 r_mcangle_it 2.609 r_mcbond_it 1.608 r_angle_refined_deg 1.47 r_angle_other_deg 0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.217 r_dihedral_angle_4_deg 15.409 r_dihedral_angle_3_deg 13.623 r_scangle_it 6.309 r_dihedral_angle_1_deg 6.17 r_scbond_it 4.545 r_mcangle_it 2.609 r_mcbond_it 1.608 r_angle_refined_deg 1.47 r_angle_other_deg 0.808 r_mcbond_other 0.382 r_symmetry_vdw_refined 0.284 r_metal_ion_refined 0.192 r_symmetry_vdw_other 0.192 r_nbd_refined 0.191 r_nbd_other 0.185 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.087 r_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5206 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 112
Software Software Software Name Purpose MolProbity model building REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing