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The structure of the P212121 crystal form of canavalin at 173 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Crystals were grown by sitting drop vapor diffusion from 18% PEG 3350 in 0.1 M HEPES reservoirs. The drops were equal amounts of a 40 mg/ml solution of precanavalin (not treated with any exogenous protease) in water. Crystals grew only after six to eight weeks at room temperature.
Crystal Properties Matthews coefficient Solvent content 2.43 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.889 α = 90 b = 90.511 β = 90 c = 183.739 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 173 PIXEL DECTRIS PILATUS3 R CdTe 300K 2018-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 2.75 60 73.4 0.282 0.275 0.29 0.07 0.998 9.9 17.2 28813 54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 8.8 0.025 0.4 2.3
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 THROUGHOUT 1CAX 2.8 30 27012 1442 78.86 0.1962 0.1933 0.2044 0.252 0.2653 RANDOM 78.346
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] -1.59 -1.34 2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.978 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 16.143 r_dihedral_angle_1_deg 7.424 r_angle_refined_deg 1.285 r_angle_other_deg 1.128 r_chiral_restr 0.042 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.978 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 16.143 r_dihedral_angle_1_deg 7.424 r_angle_refined_deg 1.285 r_angle_other_deg 1.128 r_chiral_restr 0.042 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8406 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing