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Crystal structure of the ectodomain of Drosophila transmembrane receptor PGRP-LCa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 ammonium sulphate, phosphate citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.5 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.799 α = 90 b = 105.799 β = 90 c = 105.799 γ = 90
Symmetry Space Group P 41 3 2
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 ADSC QUANTUM 315 2005-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.5 74.54 99.4 0.062 27.44 6.6 7484 7439 -3 -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 2.5 2.59 99.6 0.558 2.42 6.6 719
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 74.54 7439 7002 405 99.4 0.225 0.215 0.213 0.211 0.241 0.2423 RANDOM 51.742
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.452 r_scangle_it 2.666 r_scbond_it 1.483 r_angle_refined_deg 1.268 r_mcangle_it 1.082 r_angle_other_deg 0.803 r_mcbond_it 0.549 r_nbd_other 0.234 r_symmetry_vdw_refined 0.205 r_symmetry_vdw_other 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.452 r_scangle_it 2.666 r_scbond_it 1.483 r_angle_refined_deg 1.268 r_mcangle_it 1.082 r_angle_other_deg 0.803 r_mcbond_it 0.549 r_nbd_other 0.234 r_symmetry_vdw_refined 0.205 r_symmetry_vdw_other 0.2 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 1316 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing