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Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 30 % w/v Polyactulate 2100, sodium salt
0.2 M Ammonium Sulfate
0.1 M Hepes pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.254 α = 90 b = 103.903 β = 109.61 c = 65.326 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2017-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.65 46.86 99.74 0.06215 0.07264 0.03715 0.999 13.95 3.7 95210
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.709 99.73 0.5554 0.6521 0.3371 0.849 2.19 3.6
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 3bs8 1.65 46.91 91044 4764 99.52 0.14437 0.14281 0.1563 0.17414 0.1841 RANDOM 20.583
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] -1.49 -0.76 3.69 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.72 r_dihedral_angle_1_deg 18.15 r_dihedral_angle_4_deg 17.542 r_dihedral_angle_3_deg 13.286 r_long_range_B_refined 5.598 r_long_range_B_other 5.261 r_scangle_other 4.14 r_scbond_it 2.721 r_scbond_other 2.721 r_mcangle_it 1.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.72 r_dihedral_angle_1_deg 18.15 r_dihedral_angle_4_deg 17.542 r_dihedral_angle_3_deg 13.286 r_long_range_B_refined 5.598 r_long_range_B_other 5.261 r_scangle_other 4.14 r_scbond_it 2.721 r_scbond_other 2.721 r_mcangle_it 1.864 r_mcangle_other 1.864 r_angle_refined_deg 1.56 r_mcbond_it 1.387 r_mcbond_other 1.376 r_angle_other_deg 1.062 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_bond_other_d 0.001 r_gen_planes_refined 0.001 r_gen_planes_other 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 6386 Nucleic Acid Atoms Solvent Atoms 944 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing