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Lactaldehyde:1,2-propanediol oxidoreductase of Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O2D PDB ENTRY 1O2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PROTEIN WAS CRYSTALLIZED FROM 0.8M AMMONIUM SULPHATE, 0.1M MES PH6, pH 6.00
Crystal Properties Matthews coefficient Solvent content 3.89 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.422 α = 90 b = 109.422 β = 90 c = 182.459 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 2003-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 ESRF ID13
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 2.85 28 81.4 0.14 8.16 3.6 24555
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 2.85 2.9 67.2 0.54 2.62 3.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1O2D 2.85 28 25260 1366 88.3 0.254 0.251 0.303 RANDOM 41.75
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] 2.72 1.36 2.72 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.992 r_dihedral_angle_4_deg 24.137 r_dihedral_angle_3_deg 20.794 r_dihedral_angle_1_deg 6.344 r_scangle_it 2.433 r_angle_refined_deg 1.788 r_scbond_it 1.468 r_mcangle_it 0.887 r_mcbond_it 0.506 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.992 r_dihedral_angle_4_deg 24.137 r_dihedral_angle_3_deg 20.794 r_dihedral_angle_1_deg 6.344 r_scangle_it 2.433 r_angle_refined_deg 1.788 r_scbond_it 1.468 r_mcangle_it 0.887 r_mcbond_it 0.506 r_nbtor_refined 0.319 r_nbd_refined 0.264 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.109 r_symmetry_hbond_refined 0.029 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 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_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 5690 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XDS data scaling SCALA data scaling AMoRE phasing