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Crystal structure of 2-keto-3-deoxy-6-phospho-gluconate aldolase from Zymomonas mobilis ATCC 29191
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FQ0 PDB ENTRY 1FQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 MICROBATCH, 1 UL 10 MG/ML PROTEIN PLUS 1 UL 100 MM NAOAC/ACOH PH 4.6, 200 MM (NH4)2SO4, 30% W/V PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.6 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.38 α = 90 b = 118.05 β = 109.51 c = 55.91 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD BRUKER 2011-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER 1-MICROS
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 2.77 59.03 94.9 0.09 10.42 3.24 15242 2.5 49.2
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 2.77 2.85 94.1 0.31 2.53 2.49
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 1FQ0 2.77 7.94 15242 816 94.94 0.13729 0.13544 0.1463 0.17206 0.1814 RANDOM 40.603
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] 0.33 -0.11 0.15 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.063 r_dihedral_angle_3_deg 18.964 r_dihedral_angle_4_deg 14.521 r_dihedral_angle_1_deg 6.029 r_scbond_it 2.402 r_mcangle_it 2.247 r_angle_refined_deg 1.729 r_mcbond_it 1.339 r_mcbond_other 1.337 r_angle_other_deg 1.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.063 r_dihedral_angle_3_deg 18.964 r_dihedral_angle_4_deg 14.521 r_dihedral_angle_1_deg 6.029 r_scbond_it 2.402 r_mcangle_it 2.247 r_angle_refined_deg 1.729 r_mcbond_it 1.339 r_mcbond_other 1.337 r_angle_other_deg 1.033 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4480 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC model building XPREP data scaling MrBUMP phasing CHAINSAW phasing PHASER phasing REFMAC phasing REFMAC refinement