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Crystal structure of a cupin protein (tm1459, D50N/H52G/H92A/F104W 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 1.98 37.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.219 α = 90 b = 55.409 β = 90 c = 75.439 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 2025-11-28 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 1.595 44.66 99.6 0.053 0.998 12.3 3.48 53961
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 1.595 1.69 98.9 0.535 0.746 2.11 3.45
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 1.595 44.66 51259 2702 99.6 0.192 0.1883 0.1634 0.2636 0.2362 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 0.5024 s_from_restr_planes 0.4048 s_similar_adp_cmpnt 0.0718 s_zero_chiral_vol 0.059 s_rigid_bond_adp_cmpnt 0.0498 s_angle_d 0.0225 s_bond_d 0.0075 s_similar_dist s_anti_bump_dis_restr s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1770 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 30
Software Software Software Name Purpose PHASER phasing SHELXL refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling