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M13F/H117A/M121H Azurin with Cu(II), pH 7.4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277.15 Well buffer: 30% PEG 4000, 100 mM LiNO3, 50 mM Tris at pH 7.4
Protein stock: 1.5 mM in 25 mM Tris pH 7.8, 1.8 mM CuSO4
Crystallization drop: 1.5 uL protein stock + 1.5 uL well buffer
Crystal Properties Matthews coefficient Solvent content 2.21 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.819 α = 90 b = 48.492 β = 93.42 c = 87.983 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 PIXEL DECTRIS PILATUS3 2M 2024-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9747 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2 87.83 98.72 0.12 0.143 0.076 0.991 11.3 3.417 32803 26.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 99.12 0.574 0.681 0.362 0.751 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 87.83 1.35 32803 1660 98.72 0.2146 0.212 0.2136 0.2646 0.2261 5% 33.47
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 8.0051 f_angle_d 0.9291 f_chiral_restr 0.0536 f_bond_d 0.0075 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3896 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing