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Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GL5 PDB ENTRY 2GL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 2.4M SODIUM MALONATE, 10% GLYCEROL, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.2 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.145 α = 90 b = 135.145 β = 90 c = 135.145 γ = 90
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 MARRESEARCH MIRRORS 2006-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9794 APS 31-ID
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 2.393 36 99.6 0.085 0.081 7.6 20.3 32489 32489
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 2.393 2.52 97.2 0.562 0.59 0.9 15.2 4602
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 2GL5 2.393 20 31360 31360 1033 99.15 0.23542 0.19553 0.19403 0.1965 0.24084 0.2415 RANDOM 48.364
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.954 r_dihedral_angle_3_deg 18.169 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_1_deg 9.552 r_scangle_it 8.971 r_scbond_it 7.254 r_mcangle_it 6.64 r_mcbond_it 5.173 r_angle_refined_deg 1.235 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.954 r_dihedral_angle_3_deg 18.169 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_1_deg 9.552 r_scangle_it 8.971 r_scbond_it 7.254 r_mcangle_it 6.64 r_mcbond_it 5.173 r_angle_refined_deg 1.235 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.231 r_xyhbond_nbd_refined 0.209 r_nbd_refined 0.176 r_symmetry_vdw_refined 0.152 r_chiral_restr 0.105 r_bond_refined_d 0.009 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_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 6238 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 14
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling TRUNCATE data reduction MOLREP phasing REFMAC refinement CCP4 data scaling TRUNCATE data scaling