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Multifunctional PLP-dependent enzyme TM1270
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277.2 7.75% PEG 6000, 0.9M LiCl, 0.1M sodium citrate (pH 5.0)
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.418 α = 90 b = 120.578 β = 90 c = 137.067 γ = 90
Symmetry Space Group P 2 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 100 PIXEL DECTRIS PILATUS 2M-F 2020-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 48.12 100 0.083 0.034 0.999 15.9 6.7 96442
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 0.9 0.383 0.707 2.1 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 48.12 91439 4929 99.99 0.15142 0.15011 0.163 0.17596 0.1849 RANDOM 20.273
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] 0.7 -0.21 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.03 r_dihedral_angle_2_deg 11.697 r_long_range_B_refined 6.385 r_dihedral_angle_1_deg 6.351 r_long_range_B_other 6.331 r_scangle_other 5.346 r_scbond_it 3.51 r_scbond_other 3.509 r_mcangle_it 2.621 r_mcangle_other 2.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.03 r_dihedral_angle_2_deg 11.697 r_long_range_B_refined 6.385 r_dihedral_angle_1_deg 6.351 r_long_range_B_other 6.331 r_scangle_other 5.346 r_scbond_it 3.51 r_scbond_other 3.509 r_mcangle_it 2.621 r_mcangle_other 2.621 r_angle_refined_deg 1.902 r_mcbond_it 1.864 r_mcbond_other 1.863 r_angle_other_deg 0.662 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 6084 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing