☰ Navigation Tabs
Hexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q18 PDB ENTRY 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 Properties Matthews coefficient Solvent content 3.54 65.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.092 α = 90 b = 157.092 β = 90 c = 131.921 γ = 120
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 2005-12-07 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 99.9 99.9 0.049 30.7 5.5 50804 50804 81.7
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 2.8 100 0.526 3.4 5.5 5043
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 (All) 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 2Q18 2.7 33.74 48004 48004 2562 99.1 0.24031 0.24031 0.23808 0.2418 0.28355 0.2845 RANDOM 63.124
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] 1.89 0.95 1.89 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.128 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_4_deg 12.988 r_dihedral_angle_1_deg 5.79 r_angle_refined_deg 0.996 r_angle_other_deg 0.709 r_scangle_it 0.708 r_mcangle_it 0.546 r_mcbond_it 0.515 r_scbond_it 0.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.128 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_4_deg 12.988 r_dihedral_angle_1_deg 5.79 r_angle_refined_deg 0.996 r_angle_other_deg 0.709 r_scangle_it 0.708 r_mcangle_it 0.546 r_mcbond_it 0.515 r_scbond_it 0.451 r_nbd_refined 0.18 r_symmetry_vdw_other 0.173 r_nbtor_refined 0.165 r_nbd_other 0.162 r_symmetry_vdw_refined 0.128 r_xyhbond_nbd_refined 0.126 r_nbtor_other 0.075 r_chiral_restr 0.058 r_symmetry_hbond_refined 0.043 r_mcbond_other 0.035 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9024 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling PHASER phasing