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RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from Pseudomonas aeruginosa, apo structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DZR pdb entry 1DZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M Sodium tartrate, 0.1M MOPS, 8% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.833 α = 90 b = 57.833 β = 90 c = 161.62 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAC Science DIP-2000 2000-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS 1.5418
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 2.5 40.4 99.2 0.094 0.088 6.8 7.3 9732 9710 2.367 1.8 56.26
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) 2.5 2.67 94.4 0.455 0.419 4 6.3 1298
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1DZR 2.5 54.23 1.8 2.36 9710 9166 485 95.17 0.25 0.23326 0.23029 0.2397 0.28971 0.277 RANDOM 30.642
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] 2.35 2.35 -4.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.518 r_dihedral_angle_1_deg 5.272 r_scangle_it 3.051 r_angle_refined_deg 1.902 r_scbond_it 1.796 r_mcangle_it 1.239 r_angle_other_deg 0.905 r_symmetry_hbond_refined 0.788 r_mcbond_it 0.642 r_symmetry_vdw_other 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.518 r_dihedral_angle_1_deg 5.272 r_scangle_it 3.051 r_angle_refined_deg 1.902 r_scbond_it 1.796 r_mcangle_it 1.239 r_angle_other_deg 0.905 r_symmetry_hbond_refined 0.788 r_mcbond_it 0.642 r_symmetry_vdw_other 0.321 r_nbd_refined 0.278 r_nbd_other 0.256 r_xyhbond_nbd_other 0.253 r_symmetry_vdw_refined 0.241 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_other 0.149 r_nbtor_other 0.109 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_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 1490 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing