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Crystal structure of a putative lyase/mutase from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZE3 PDB entry 2ZE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 20% PEG 8000, 0.2M MgCl2, Tris HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.06 α = 90 b = 70.03 β = 90 c = 141.86 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 MARMOSAIC 300 mm CCD 2013-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9798 APS 21-ID-F
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 1.8 50 97.2 0.064 18.6 5 48518 14.3
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 1.8 1.85 98.5 0.466 3.3 4.97 3583
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 2ZE3 1.8 47.33 45828 2440 96.8 0.16895 0.16674 0.1815 0.21081 0.2184 RANDOM 22.274
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] 3.16 -1.39 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.325 r_dihedral_angle_4_deg 15.041 r_dihedral_angle_3_deg 12.392 r_dihedral_angle_1_deg 5.708 r_long_range_B_refined 4.951 r_long_range_B_other 4.769 r_scangle_other 2.882 r_mcangle_other 2.065 r_mcangle_it 2.064 r_scbond_it 1.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.325 r_dihedral_angle_4_deg 15.041 r_dihedral_angle_3_deg 12.392 r_dihedral_angle_1_deg 5.708 r_long_range_B_refined 4.951 r_long_range_B_other 4.769 r_scangle_other 2.882 r_mcangle_other 2.065 r_mcangle_it 2.064 r_scbond_it 1.881 r_scbond_other 1.878 r_angle_refined_deg 1.568 r_mcbond_it 1.338 r_mcbond_other 1.334 r_angle_other_deg 0.852 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3986 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 4
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling