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Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/H54A/C106D mutant) in copper (Cu) substituted form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 26-28% w/v Jeffamine ED-2001, 0.1M MES pH6.0
Crystal Properties Matthews coefficient Solvent content 1.98 37.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.57 α = 90 b = 58.5 β = 90 c = 71.96 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2023-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.07 50 98.5 0.997 14.7 3.32 176945
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.07 1.14 95.6 0.806 2.1 2.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.07 50 176945 9819 89.5 0.1385 0.137 0.1238 0.163 0.1489 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 29
RMS Deviations Key Refinement Restraint Deviation s_from_restr_planes 0.4343 s_rigid_bond_adp_cmpnt 0.2864 s_non_zero_chiral_vol 0.1543 s_similar_adp_cmpnt 0.1361 s_zero_chiral_vol 0.08 s_angle_d 0.026 s_bond_d 0.013 s_similar_dist s_anti_bump_dis_restr s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8694 Nucleic Acid Atoms Solvent Atoms 844 Heterogen Atoms 58
Software Software Software Name Purpose PHASER phasing SHELXL-97 refinement XDS data reduction XDS data scaling