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H117A/M121H Azurin with Cu(II), pH 7.7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 277 Well buffer: 27% PEG 4000, 100 mM LiNO3, 50 mM Tris at pH 7.7
Protein stock: 1.5 mM in 25 mM Tris pH 7.8, 1.8 mM CuSO4
Crystallization drop: 1 uL protein stock + 3 uL well buffer
Crystal Properties Matthews coefficient Solvent content 2.1 41.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.905 α = 90 b = 48.836 β = 90 c = 81.31 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 2024-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0332 ALS 8.2.2
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 2.04 81.31 99.26 0.148 0.175 0.094 0.979 6.3 3.36 29554 19.57
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 2.04 2.07 96.26 0.548 0.662 0.365 0.269 1.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.04 81.31 1.34 29488 1474 99.03 0.1791 0.1764 0.1766 0.2328 0.233 21.72
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 7.6723 f_angle_d 0.8397 f_chiral_restr 0.0501 f_bond_d 0.0066 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3884 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing