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Crystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase from Bruciella melitensis at 1.85A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FWS pdb coordinate set 1fws, monomer after sidechain adjustment with chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 JCSG+ SCREEN D3: 100MM NA/K PHOSPHATE PH 6.2, 50% PEG 200, 200MM NACL, PH 5.5, VAPOR DIFFUSION, TEMPERATURE 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.53 α = 90 b = 75.64 β = 126 c = 74.65 γ = 90
Symmetry Space Group C 1 2 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 WESTBROOK NOIR 2008-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
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 1.85 50 97.7 0.078 10.22 3.5 45916 45916 -3 29.4
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) 1.85 1.9 87.1 0.481 2.6 2.6 3021
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MR THROUGHOUT pdb coordinate set 1fws, monomer after sidechain adjustment with chainsaw 1.85 19.17 45914 45914 2366 98.3 0.179 0.179 0.176 0.1825 0.222 0.2255 RANDOM 20.39
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] -0.18 0.18 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.924 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_1_deg 5.994 r_scangle_it 4.376 r_scbond_it 2.682 r_mcangle_it 1.773 r_angle_refined_deg 1.591 r_mcbond_it 1.007 r_angle_other_deg 0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.924 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_1_deg 5.994 r_scangle_it 4.376 r_scbond_it 2.682 r_mcangle_it 1.773 r_angle_refined_deg 1.591 r_mcbond_it 1.007 r_angle_other_deg 0.993 r_mcbond_other 0.275 r_chiral_restr 0.097 r_bond_refined_d 0.017 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3778 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 40
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling