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Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia ambifaria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 EBS internal tracking number 224045c2 WIZARD 3/4 C2.
24%(w/v) PEG 1500, 20%(v/v) Glycerol, BuamA.00102.a.A1 PS01117 at 74 mg/mL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.32 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.13 α = 90 b = 129.5 β = 90 c = 169.39 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 RIGAKU SATURN 944+ 2011-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.95 45.94 98.9 0.087 12.71 6.1 79104 -3 30.992
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 1.95 2 89.8 0.401 2.4 2.8
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 MR THROUGHOUT 3SZ8 1.95 44.33 78773 3951 98.62 0.172 0.17 0.1744 0.203 0.2071 RANDOM 28.114
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] 0.5 0.43 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.003 r_dihedral_angle_4_deg 21.176 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_1_deg 5.475 r_angle_refined_deg 1.494 r_angle_other_deg 0.969 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.003 r_dihedral_angle_4_deg 21.176 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_1_deg 5.475 r_angle_refined_deg 1.494 r_angle_other_deg 0.969 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7890 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction