☰ Navigation Tabs
Structure of truncated Norcoclaurine Synthase from Thalictrum flavum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQ5 2VQ5 CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 10% w/v polyethylene glycol 1000, 10% w/v polyethylene glycol 8000 20 mM Tris, 50 mM NaCl, ph 7.5
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.046 α = 90 b = 109.632 β = 90 c = 136.739 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 PILATUS3 S 6M 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.970 SOLEIL PROXIMA 1
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 2 109.63 99.3 0.147 6.1 5.4 39359 27.34
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 2.05 99.7 1.141 1.7 5.5
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 2VQ5 CHAIN A 2 85.68 37264 1960 98.8 0.199 0.197 0.2077 0.236 0.2432 RANDOM 35.54
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] 0.15 0.86 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.049 r_dihedral_angle_3_deg 13.754 r_long_range_B_refined 6.824 r_long_range_B_other 6.686 r_dihedral_angle_1_deg 6.256 r_scangle_other 3.238 r_dihedral_angle_4_deg 2.761 r_mcangle_other 2.644 r_mcangle_it 2.643 r_angle_refined_deg 2.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.049 r_dihedral_angle_3_deg 13.754 r_long_range_B_refined 6.824 r_long_range_B_other 6.686 r_dihedral_angle_1_deg 6.256 r_scangle_other 3.238 r_dihedral_angle_4_deg 2.761 r_mcangle_other 2.644 r_mcangle_it 2.643 r_angle_refined_deg 2.078 r_scbond_it 2.058 r_scbond_other 2.057 r_mcbond_it 1.662 r_mcbond_other 1.652 r_angle_other_deg 1.058 r_chiral_restr 0.132 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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 3703 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing