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Crystal structure of a cupin protein (tm1459, R39K/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound 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 6 293 25% w/v Jeffamine ED-2001, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.08 40.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.148 α = 90 b = 58.096 β = 90 c = 74.539 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 2025-11-07 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 1.087 50 98.6 0.058 0.994 12.8 3.4 174458
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 1.087 1.15 95.4 0.183 0.962 4.89 3.5
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 1.087 50 174458 8698 98.6 0.1331 0.1331 0.1317 0.1271 0.1605 0.1504 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_non_zero_chiral_vol 0.6644 s_from_restr_planes 0.437 s_approx_iso_adps 0.1482 s_zero_chiral_vol 0.1189 s_similar_adp_cmpnt 0.0533 s_rigid_bond_adp_cmpnt 0.0295 s_angle_d 0.0262 s_bond_d 0.0124 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3779 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms
Software Software Software Name Purpose SHELXL refinement PHASER phasing PDB_EXTRACT data extraction XDS data reduction XDS data scaling