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Pyranose 2-oxidase F454N mutant in complex with 2FG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IGO pdb entry 2IGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 0.1M MES, 50MM MGCL2, 10% (W/V)% MONOMETHYLETHER PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.572 α = 90 b = 101.572 β = 90 c = 250.052 γ = 90
Symmetry Space Group P 43 21 2
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 MARRESEARCH MIRRORS 2008-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0379 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 30 99.9 0.102 15.4 7.3 132005 132005
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 99.9 0.883 2.5 7.3 10540
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 2IGO 1.75 30 130031 130031 1974 99.91 0.17596 0.17596 0.17544 0.1821 0.20943 0.2147 RANDOM 13.25
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] -0.24 -0.24 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.74 r_dihedral_angle_4_deg 13.73 r_dihedral_angle_3_deg 13.301 r_dihedral_angle_1_deg 6.742 r_scangle_it 3.887 r_scbond_it 2.809 r_angle_refined_deg 1.991 r_mcangle_it 1.685 r_mcbond_it 1.43 r_angle_other_deg 1.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.74 r_dihedral_angle_4_deg 13.73 r_dihedral_angle_3_deg 13.301 r_dihedral_angle_1_deg 6.742 r_scangle_it 3.887 r_scbond_it 2.809 r_angle_refined_deg 1.991 r_mcangle_it 1.685 r_mcbond_it 1.43 r_angle_other_deg 1.036 r_mcbond_other 0.35 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.232 r_xyhbond_nbd_other 0.227 r_symmetry_vdw_other 0.226 r_chiral_restr 0.222 r_nbd_other 0.211 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.13 r_nbtor_other 0.093 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8944 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms 166
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling