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Crystal structure of PAP-S1aci, a pokeweed antiviral protein from seeds of Phytolacca acinosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PAF PDB ENTRY 1PAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 289 Drop: 4 uL 20mg/ml protein, 4 uL 42-44% PEG 4K, 2 uL 1M sodium citrate, 100 mM phosphate buffer, pH 7.2
Reservoir: 1000 uL 42-44% PEG 4K in 100 mM phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.63 α = 90 b = 84.19 β = 90 c = 90.88 γ = 90
Symmetry Space Group I 2 2 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 MAR CCD 165 mm 2001-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8033 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 30 99.9 0.043 55.7 12.4 33627 33596 -3 20.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 100 0.389 7.1 12.4 2194
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-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 1PAF 1.7 29.73 32752 1625 97.7 0.169 0.1768 0.211 0.2174 RANDOM 26.8
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] 6.65 -8.28 1.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 4.38 c_scbond_it 3.04 c_mcangle_it 2.25 c_angle_deg 1.7 c_mcbond_it 1.46 c_improper_angle_d 1.02 c_bond_d 0.012 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 4.38 c_scbond_it 3.04 c_mcangle_it 2.25 c_angle_deg 1.7 c_mcbond_it 1.46 c_improper_angle_d 1.02 c_bond_d 0.012 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 2061 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 14
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing