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Crystal structure of YxaG, a dioxygenase from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQG PDB Entry 1GQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Sodium Hepes, PEG 400, Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.93 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.417 α = 90 b = 128.425 β = 90 c = 51.189 γ = 90
Symmetry Space Group P 21 21 2
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 4 2002-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 20 98.2 0.089 20.37 6.01 33292 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.5 94.3
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 1GQG 2.4 91.29 31547 1696 97.54 0.22013 0.21704 0.2214 0.27679 0.2779 RANDOM 37.9
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] -0.99 -3.04 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.862 r_scangle_it 5.693 r_scbond_it 3.765 r_angle_refined_deg 2.996 r_mcangle_it 2.799 r_angle_other_deg 2.13 r_mcbond_it 1.691 r_nbd_other 0.323 r_symmetry_vdw_refined 0.313 r_nbd_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.862 r_scangle_it 5.693 r_scbond_it 3.765 r_angle_refined_deg 2.996 r_mcangle_it 2.799 r_angle_other_deg 2.13 r_mcbond_it 1.691 r_nbd_other 0.323 r_symmetry_vdw_refined 0.313 r_nbd_refined 0.295 r_xyhbond_nbd_refined 0.284 r_symmetry_vdw_other 0.276 r_chiral_restr 0.211 r_gen_planes_other 0.162 r_nbtor_other 0.145 r_bond_other_d 0.13 r_gen_planes_refined 0.084 r_bond_refined_d 0.047 r_symmetry_hbond_refined 0.023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5141 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing