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Crystal structure of the complex formed between type 1 ribosome inactivating protein and adenine at 1.7A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AHA PDB ENTRY 1AHA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.207 α = 90 b = 130.207 β = 90 c = 39.831 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH mirror 2011-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 1.7 65 99 0.04 47 26234 26234 28.7
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 1.7 1.74 99.6 0.618 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1AHA 1.7 37.59 26234 26234 1409 99.96 0.17629 0.17628 0.17463 0.1739 0.20868 0.2071 RANDOM 33.148
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] -1.09 -0.54 -1.09 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.186 r_dihedral_angle_4_deg 21.162 r_dihedral_angle_3_deg 13.022 r_dihedral_angle_1_deg 5.137 r_angle_refined_deg 1.476 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling