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Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in complexes with sodium and chloride ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 Tacsimate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.119 α = 90 b = 109.065 β = 98.83 c = 95.017 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2016-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 19.64 96 0.08 0.08 6.6 3.58 80576
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 1.8 1.86 93.3 0.514 1.8 3.54
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 5T1F 1.8 19.64 76559 4016 95.95 0.212 0.2092 0.2135 0.2657 0.2624 RANDOM 32.891
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_4_deg 19.802 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_1_deg 8.379 r_angle_refined_deg 0.858 r_angle_other_deg 0.527 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_4_deg 19.802 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_1_deg 8.379 r_angle_refined_deg 0.858 r_angle_other_deg 0.527 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6660 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms 123
Software Software Software Name Purpose CrystalClear data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing d*TREK data scaling CrystalClear data reduction