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Crystal structure of the Drosophila pattern-recognition receptor PGRP-SA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OHT PDB code 1OHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 294 sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.733 α = 90 b = 49.431 β = 101.03 c = 69.83 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD CUSTOM-MADE 2003-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.91963 APS 19-ID
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 2.2 50 99.7 0.087 18.6 3.5 20080 -3 31.5
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) 2.2 2.24 95 0.14 387.9 3 946
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 code 1OHT 2.2 48.8 19013 18097 916 95.45 0.19572 0.19572 0.1934 0.1957 0.24179 0.243 RANDOM 27.546
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] 0.59 -0.67 -1.37 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.177 r_scangle_it 3.279 r_scbond_it 2.017 r_angle_refined_deg 1.331 r_mcangle_it 1.296 r_mcbond_it 0.662 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.177 r_scangle_it 3.279 r_scbond_it 2.017 r_angle_refined_deg 1.331 r_mcangle_it 1.296 r_mcbond_it 0.662 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2622 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing