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Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia Xenovorans LB400 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 277 0.2M Li2SO4, 20.0% PEG-3350, No Buffer, pH 6.4, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.97 α = 90 b = 88.304 β = 90 c = 88.571 γ = 90
Symmetry Space Group C 2 2 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 315 2006-09-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000, 0.9795, 0.9792 ALS 8.2.2
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 1.7 27.692 98 0.128 0.128 8.3 3.4 30205 14.9
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) 1.7 1.74 97.4 0.916 0.916 1.7 3.5 2176
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.7 27.692 30193 1538 97.49 0.179 0.176 0.1843 0.22 0.2275 RANDOM 11.044
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] -0.71 1.58 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.653 r_dihedral_angle_4_deg 13.11 r_dihedral_angle_3_deg 11.599 r_dihedral_angle_1_deg 6.428 r_scangle_it 6.24 r_scbond_it 4.395 r_mcangle_it 2.702 r_mcbond_it 2.119 r_angle_refined_deg 1.466 r_angle_other_deg 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.653 r_dihedral_angle_4_deg 13.11 r_dihedral_angle_3_deg 11.599 r_dihedral_angle_1_deg 6.428 r_scangle_it 6.24 r_scbond_it 4.395 r_mcangle_it 2.702 r_mcbond_it 2.119 r_angle_refined_deg 1.466 r_angle_other_deg 0.967 r_mcbond_other 0.562 r_symmetry_vdw_other 0.281 r_nbd_other 0.204 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.192 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.157 r_nbtor_other 0.089 r_chiral_restr 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1884 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 25
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing