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Crystal structure of a HpcH/Hpal aldolase/citrate lyase family protein from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DXE PDB entry 1DXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 JCSG+a9: 20% PEG3350, 0.2M AmCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.11 α = 90 b = 116.48 β = 90 c = 161.66 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 225 mm CCD 2013-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 2 50 99.9 0.075 21.7 6 95233 95110 16.7
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 2 2.05 100 0.448 4.15 6.15 6950
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 1DXE 2 48.95 90266 4765 99.87 0.16702 0.16457 0.1751 0.21254 0.2192 RANDOM 21.775
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] 0.09 -0.68 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.23 r_dihedral_angle_4_deg 19.439 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.585 r_long_range_B_refined 4.976 r_long_range_B_other 4.976 r_scangle_other 3.04 r_mcangle_it 1.986 r_mcangle_other 1.986 r_scbond_it 1.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.23 r_dihedral_angle_4_deg 19.439 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.585 r_long_range_B_refined 4.976 r_long_range_B_other 4.976 r_scangle_other 3.04 r_mcangle_it 1.986 r_mcangle_other 1.986 r_scbond_it 1.936 r_scbond_other 1.935 r_angle_refined_deg 1.56 r_mcbond_it 1.274 r_mcbond_other 1.273 r_angle_other_deg 0.855 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 11468 Nucleic Acid Atoms Solvent Atoms 967 Heterogen Atoms 20
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling