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The X-ray structure of Apis mellifera PGRP-SA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1 M TRIS hydrochloride; 2.0 M Ammonium sulfate; PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.898 α = 90 b = 68.607 β = 94.92 c = 71.699 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 100 CCD ADSC QUANTUM 315r 2016-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 50.01 91.3 9.4 7.4 50577
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-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 1S2J 1.86 50.01 48086 2476 90.93 0.19138 0.18993 0.1903 0.21655 0.2166 RANDOM 36.016
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] 1.76 0.31 0.08 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.921 r_dihedral_angle_3_deg 15.656 r_dihedral_angle_4_deg 13.041 r_dihedral_angle_1_deg 6.294 r_long_range_B_refined 3.803 r_mcangle_it 1.473 r_angle_refined_deg 1.357 r_scbond_it 1.333 r_mcbond_it 0.931 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.921 r_dihedral_angle_3_deg 15.656 r_dihedral_angle_4_deg 13.041 r_dihedral_angle_1_deg 6.294 r_long_range_B_refined 3.803 r_mcangle_it 1.473 r_angle_refined_deg 1.357 r_scbond_it 1.333 r_mcbond_it 0.931 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5361 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing