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M13F/G116F Pseudomonas aeruginosa azurin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 The 1.4 mM apo-protein was prepared in 100 mM pH=5.6 NaOAc buffer. For each well, add 300 uL reservoir buffer containing 100 mM pH=8.0 Tris-HCl, 10 mM CuSO4 and 20% PEG-4000. 3 uL of protein stock was mixed with 1 uL reservoir buffer on the glass slides and sealed on the wells. Diamond-shaped blue crystals grew within 4 days.
Crystal Properties Matthews coefficient Solvent content 2.51 51.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.274 α = 90 b = 73.901 β = 90 c = 77.616 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS PILATUS3 6M 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.47 41 99 0.09367 0.103 0.995 8.87 6 24023 14.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.523 0.3451 0.3949 0.891 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4azu 1.47 41 1.34 24023 2350 96.11 0.2061 0.2044 0.1999 0.2373 0.2323 22.48
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 f_dihedral_angle_d 15.6121 f_angle_d 0.8646 f_chiral_restr 0.0812 f_bond_d 0.0058 f_plane_restr 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 984 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing