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Crystal Structure of sylvaticin, a new secreted protein from pythium sylvaticum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Sylvaticin C2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 40% PEG 2000MME, 10mM NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.22 α = 85.2 b = 46 β = 71.27 c = 55.73 γ = 74.63
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 4 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 33 92 0.048 0.041 18.1 2 43901 40560 1 17.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.59 1.69 91.3 0.12 0.1 9.22 2 6468
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Sylvaticin C2 1.6 21.06 43341 40262 2024 92.9 0.152 0.152 0.15 0.1562 0.187 RANDOM 19.769
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.403 r_dihedral_angle_3_deg 11.806 r_dihedral_angle_4_deg 6.956 r_dihedral_angle_1_deg 4.767 r_scangle_it 2.647 r_scbond_it 1.61 r_angle_refined_deg 1.11 r_mcangle_it 0.897 r_mcbond_it 0.497 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.403 r_dihedral_angle_3_deg 11.806 r_dihedral_angle_4_deg 6.956 r_dihedral_angle_1_deg 4.767 r_scangle_it 2.647 r_scbond_it 1.61 r_angle_refined_deg 1.11 r_mcangle_it 0.897 r_mcbond_it 0.497 r_nbtor_refined 0.307 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.109 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_metal_ion_refined 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2930 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 37
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction XDS data scaling