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2-keto-3-deoxy-D-arabinonate dehydratase apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 Na/K phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.93 α = 90 b = 128.93 β = 90 c = 225.09 γ = 90
Symmetry Space Group I 41 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 3 15 95.9 0.116 9.5 4.4 18610 18610
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 3 3.1 99.5 0.381 3.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2Q18 3 14.96 17680 17680 926 96.85 0.21591 0.21449 0.2128 0.24319 0.2425 RANDOM 44.001
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] 2.01 2.01 -4.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.014 r_dihedral_angle_4_deg 14.19 r_dihedral_angle_3_deg 14.121 r_dihedral_angle_1_deg 5.34 r_scangle_it 1.099 r_angle_refined_deg 1.064 r_mcangle_it 0.75 r_scbond_it 0.625 r_mcbond_it 0.421 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.014 r_dihedral_angle_4_deg 14.19 r_dihedral_angle_3_deg 14.121 r_dihedral_angle_1_deg 5.34 r_scangle_it 1.099 r_angle_refined_deg 1.064 r_mcangle_it 0.75 r_scbond_it 0.625 r_mcbond_it 0.421 r_nbtor_refined 0.302 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.137 r_symmetry_vdw_refined 0.131 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling XFIT data reduction