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Structure of a Transaldolase from Oleispira antarctica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ONR PDB entry 1ONR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 4M sodium formate, 3mM magnesium chloride, cryoprotected in Paratone-N oil (Hampton), VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 8.5
Crystal Properties Matthews coefficient Solvent content 4.88 74.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.105 α = 90 b = 143.105 β = 90 c = 119.724 γ = 120
Symmetry Space Group P 61 2 2
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 ADSC QUANTUM 210r Mirrors 2009-06-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97942, 0.97972 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.8 35.78 99.9 0.088 0.088 57.4 26.2 18484 18469 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 98.9 0.734 0.734 4.9 25.8
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1ONR 2.79 35.78 17475 947 99.82 0.21114 0.20914 0.2068 0.24886 0.2487 RANDOM 71.242
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] 0.04 0.02 0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.726 r_dihedral_angle_4_deg 23.341 r_dihedral_angle_3_deg 20.289 r_dihedral_angle_1_deg 6.614 r_angle_refined_deg 1.468 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.3 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.726 r_dihedral_angle_4_deg 23.341 r_dihedral_angle_3_deg 20.289 r_dihedral_angle_1_deg 6.614 r_angle_refined_deg 1.468 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.3 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.098 r_symmetry_hbond_refined 0.065 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 2503 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-2000 data scaling