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Crystal structure of a cupin protein (tm1459, H54AH58A 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 6 293 25%(w/v) Jeffamine ED-2001, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.05 39.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.635 α = 90 b = 57.797 β = 90 c = 74.402 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 CCD RAYONIX MX300HE 2016-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.23 50 100 0.076 0.081 0.03 29.4 7.2 63984
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 1.23 1.25 99.9 0.971 0.032 0.012 0.999 3.27 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5WSD 1.23 30 60710 3202 100 0.146 0.146 0.1315 0.1881 0.1595 RANDOM 18.9856
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 0.709 s_from_restr_planes 0.394 s_approx_iso_adps 0.127 s_zero_chiral_vol 0.061 s_similar_adp_cmpnt 0.046 s_rigid_bond_adp_cmpnt 0.027 s_angle_d 0.023 s_bond_d 0.007 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1827 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 38
Software Software Software Name Purpose HKL-2000 data scaling SHELX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing