☰ Navigation Tabs
old yellow enzymes-Q102A/Y169F/R215A/R308A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 glycine,PEG 2000,glycerinum
Crystal Properties Matthews coefficient Solvent content 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.06 α = 90 b = 143.57 β = 90 c = 155.47 γ = 90
Symmetry Space Group I 21 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 Bruker PHOTON II MULTILAYER 2023-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.11 45.74 98.9 0.175 0.967 5.8 3.5 17476
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 3.11 3.32 0.494
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 3.11 45.74 17476 881 98.9 0.21757 0.21513 0.2193 0.26484 0.2646 RANDOM 35.835
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] 4.85 -1.74 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_4_deg 13.983 r_dihedral_angle_1_deg 5.594 r_long_range_B_refined 4.71 r_long_range_B_other 4.709 r_mcangle_it 2.317 r_mcangle_other 2.317 r_scangle_other 2.022 r_angle_refined_deg 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_4_deg 13.983 r_dihedral_angle_1_deg 5.594 r_long_range_B_refined 4.71 r_long_range_B_other 4.709 r_mcangle_it 2.317 r_mcangle_other 2.317 r_scangle_other 2.022 r_angle_refined_deg 1.453 r_mcbond_it 1.323 r_mcbond_other 1.321 r_scbond_it 1.197 r_scbond_other 1.145 r_angle_other_deg 0.726 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 5270 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 45
Software Software Software Name Purpose PRIME-X refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing