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Agglutinin from Abrus Precatorius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ABR PDB ENTRY 1ABR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 6.5% PEG 8000, 1% SODIUM AZIDE, 0.1M TRIS BUFFER, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 8.0
Crystal Properties Matthews coefficient Solvent content 4.45 72.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.05 α = 90 b = 137.05 β = 90 c = 214.424 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 4r 2004-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.0000 SPring-8 BL12B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.47 30 99.1 0.072 11.9 4.1 73976 50.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.56 98.1 0.36 1.8 3.6
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 PDB ENTRY 1ABR 2.6 19.88 63111 6301 99.8 0.199 0.199 0.2073 0.227 0.2385 RANDOM 49.3
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] 1.81 1.81 -3.62
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.4 c_scangle_it 3.9 c_scbond_it 2.87 c_mcangle_it 2.84 c_mcbond_it 1.87 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.4 c_scangle_it 3.9 c_scbond_it 2.87 c_mcangle_it 2.84 c_mcbond_it 1.87 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8060 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing