☰ Navigation Tabs
Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYH PDB entry 2NYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 NANODROP, 0.2M NaCl, 10.0% PEG 3000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.835 α = 90 b = 138.772 β = 98.43 c = 44.046 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98086 SSRL BL11-1
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 1.4 30.002 85 0.071 0.071 6.9 3.2 85722 13.21
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 1.4 1.44 82.3 0.466 0.466 1.7 2.2 6121
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 2NYH 1.4 30.002 85675 4342 84.29 0.145 0.145 0.144 0.1525 0.173 0.1804 RANDOM 12.313
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] 0.55 -0.25 -0.21 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.258 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 11.087 r_dihedral_angle_1_deg 6.132 r_scangle_it 5.656 r_scbond_it 3.829 r_mcangle_it 2.349 r_mcbond_it 1.864 r_angle_refined_deg 1.555 r_angle_other_deg 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.258 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 11.087 r_dihedral_angle_1_deg 6.132 r_scangle_it 5.656 r_scbond_it 3.829 r_mcangle_it 2.349 r_mcbond_it 1.864 r_angle_refined_deg 1.555 r_angle_other_deg 0.814 r_mcbond_other 0.436 r_symmetry_vdw_other 0.27 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.199 r_nbd_other 0.192 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.089 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3771 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms 57
Software Software Software Name Purpose MolProbity model building REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing