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Crystal structure of a cupin protein (tm1459, presequence-truncated H52A mutant) soaked in CuSO4
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 6 293 25% w/v Jeffamine ED-2001, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.95 58.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.215 α = 90 b = 52.215 β = 90 c = 98.314 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M 2025-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.899995 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.162 45.22 100 0.034 0.999 18.46 5.11 103335
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.162 1.23 99.9 0.63 0.78 2.07 4.88
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 (All) 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 1.162 45.22 98153 5182 100 0.1473 0.1473 0.146 0.1335 0.1727 0.1524 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]
RMS Deviations Key Refinement Restraint Deviation s_from_restr_planes 0.4204 s_similar_adp_cmpnt 0.1705 s_zero_chiral_vol 0.1084 s_non_zero_chiral_vol 0.0765 s_rigid_bond_adp_cmpnt 0.0325 s_angle_d 0.0247 s_bond_d 0.0119 s_similar_dist s_anti_bump_dis_restr s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 920 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 9
Software Software Software Name Purpose PHASER phasing SHELXL refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling