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Crystal structure of NADH-dependent reductase A1-R' responsible for alginate metabolism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 PEG 400, sodium/potassium phosphate, sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.717 α = 90 b = 87.717 β = 90 c = 139.598 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 100 CCD ADSC QUANTUM 315 2013-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.8 50 100 0.06 47.3 11.7 58400 -3 17.4
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 1.8 1.86 100 0.384 5.8 11.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3AFM 1.8 33.39 55375 2949 99.82 0.18216 0.18128 0.1908 0.19944 0.2085 RANDOM 24.577
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] 0.49 0.49 0.49 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.011 r_dihedral_angle_4_deg 14.96 r_dihedral_angle_3_deg 10.389 r_dihedral_angle_1_deg 5.414 r_long_range_B_refined 4.106 r_long_range_B_other 3.72 r_scangle_other 1.635 r_mcangle_it 1.454 r_mcangle_other 1.454 r_angle_refined_deg 1.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.011 r_dihedral_angle_4_deg 14.96 r_dihedral_angle_3_deg 10.389 r_dihedral_angle_1_deg 5.414 r_long_range_B_refined 4.106 r_long_range_B_other 3.72 r_scangle_other 1.635 r_mcangle_it 1.454 r_mcangle_other 1.454 r_angle_refined_deg 1.157 r_scbond_it 0.963 r_scbond_other 0.959 r_mcbond_it 0.823 r_mcbond_other 0.823 r_angle_other_deg 0.712 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3607 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement