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The structure of the orthorhombic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 The crystal was grown at 4 degrees C in PACT condition B12 (0.01 M zinc chloride, 0.1 M MES pH 6, 20 % PEG 6000).
Crystal Properties Matthews coefficient Solvent content 3.32 62.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.589 α = 90 b = 95.47 β = 90 c = 96.339 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 PILATUS 6M 2015-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.77 67.8 99.7 0.106 0.11 0.999 14.8 13.3 72825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.81 99.3 2.552 2.661 0.629 1 12.5
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 47.735 69469 3452 99.97 0.1823 0.2333 0.2211 39.79
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] 0.974573188 -16.04594 15.0713668
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 13.8854 s_dihedral_angle_3_deg 10.7443 s_dihedral_angle_1_deg 6.9966 s_dihedral_angle_2_deg 4.5435 s_angle_nonh_deg 2.0041 s_hbond_nbd 0.2465 s_nbd 0.2308 s_nbtor 0.2244 s_symmetry_nbd 0.1782 s_symmetry_hbond_nbd 0.1734
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 13.8854 s_dihedral_angle_3_deg 10.7443 s_dihedral_angle_1_deg 6.9966 s_dihedral_angle_2_deg 4.5435 s_angle_nonh_deg 2.0041 s_hbond_nbd 0.2465 s_nbd 0.2308 s_nbtor 0.2244 s_symmetry_nbd 0.1782 s_symmetry_hbond_nbd 0.1734 s_metal_ion 0.1143 s_chiral_restr 0.0871 s_bond_nonh_d 0.0121 s_planes 0.0093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3919 Nucleic Acid Atoms Solvent Atoms 680 Heterogen Atoms 118
Software Software Software Name Purpose Servalcat refinement iMOSFLM data reduction SCALA data scaling PHASER phasing