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2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate
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 = 128.28 α = 90 b = 128.28 β = 90 c = 223.52 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 2006-11-01 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 2.7 20 97.3 0.071 11.4 4.1 25301 25301
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 2.7 2.8 93.4 0.281 4.1
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 2.7 19.58 24400 24400 1284 99.1 0.22809 0.22638 0.2258 0.26077 0.2566 RANDOM 49.816
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] 1.58 1.58 -3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.616 r_dihedral_angle_4_deg 17.532 r_dihedral_angle_3_deg 15.463 r_dihedral_angle_1_deg 5.998 r_scangle_it 2.162 r_angle_refined_deg 1.322 r_scbond_it 1.239 r_mcangle_it 1.084 r_mcbond_it 0.6 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.616 r_dihedral_angle_4_deg 17.532 r_dihedral_angle_3_deg 15.463 r_dihedral_angle_1_deg 5.998 r_scangle_it 2.162 r_angle_refined_deg 1.322 r_scbond_it 1.239 r_mcangle_it 1.084 r_mcbond_it 0.6 r_nbtor_refined 0.313 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.082 r_metal_ion_refined 0.053 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_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 2227 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling XFIT data reduction