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The structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEP PDB ENTRY 1KEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 30% PEG 4K, 0.1M CITRIC ACID, PH5.4, 0.3M AMMONIUM SULPHATE,, pH 5.40
Crystal Properties Matthews coefficient Solvent content 3.5 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.41 α = 90 b = 94.829 β = 90 c = 183.543 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD MIRRORS 2001-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.5 91.28 98.6 0.116 4.3 3.5 179804
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 1.1 1.53 98.6 0.66 1.2 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KEP 1.5 91.29 152105 16689 98.3 0.173 0.17 0.1843 0.2 0.2075 RANDOM 15.63
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] 0.05 1.36 -1.41
RMS Deviations Key Refinement Restraint Deviation r_chiral_restr 6.06 r_scangle_it 4.653 r_scbond_it 3.225 r_mcangle_it 2.212 r_angle_other_deg 1.861 r_dihedral_angle_1_deg 1.821 r_mcbond_it 1.565 r_symmetry_hbond_refined 0.648 r_symmetry_vdw_other 0.355 r_nbd_other 0.27
RMS Deviations Key Refinement Restraint Deviation r_chiral_restr 6.06 r_scangle_it 4.653 r_scbond_it 3.225 r_mcangle_it 2.212 r_angle_other_deg 1.861 r_dihedral_angle_1_deg 1.821 r_mcbond_it 1.565 r_symmetry_hbond_refined 0.648 r_symmetry_vdw_other 0.355 r_nbd_other 0.27 r_nbd_refined 0.257 r_symmetry_vdw_refined 0.25 r_xyhbond_nbd_refined 0.206 r_nbtor_other 0.09 r_gen_planes_other 0.02 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.008 r_angle_refined_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5479 Nucleic Acid Atoms Solvent Atoms 757 Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling AMoRE phasing