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Structure of glycolate oxidase containing FMN from Nicotiana benthamiana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 35%(w/v) MPD, 0.2M ammonium acetate, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.15 70.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.23 α = 90 b = 144.23 β = 90 c = 129.823 γ = 90
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 270 2014-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
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 2.8 50 90 0.1 12 5 32743 3
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 2.8 2.85 90.9 0.255 4.77 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 1GOX 2.8 45.61 27661 1496 89.05 0.17162 0.17072 0.1696 0.18815 0.1838 RANDOM 43.203
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] -2.23 -2.23 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.517 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 15.323 r_dihedral_angle_1_deg 6.44 r_long_range_B_refined 4.438 r_long_range_B_other 4.392 r_mcangle_it 2.263 r_mcangle_other 2.263 r_scangle_other 2.128 r_mcbond_it 1.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.517 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 15.323 r_dihedral_angle_1_deg 6.44 r_long_range_B_refined 4.438 r_long_range_B_other 4.392 r_mcangle_it 2.263 r_mcangle_other 2.263 r_scangle_other 2.128 r_mcbond_it 1.345 r_mcbond_other 1.344 r_angle_refined_deg 1.267 r_scbond_it 1.257 r_scbond_other 1.257 r_angle_other_deg 0.921 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5388 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing