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High-resolution crystal structure of Fc bound to its human receptor Fc-gamma-RI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6X 1L6X and 3RJD experimental model PDB 3RJD 1L6X and 3RJD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1M sodium acetate, 0.1 M zinc acetate, 4% 1,4-butanediol, 12% PEG 4,000
Crystal Properties Matthews coefficient Solvent content 3.26 62.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.98 α = 90 b = 126.5 β = 118.95 c = 71.61 γ = 90
Symmetry Space Group C 1 2 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 315 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 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 1.8 39.7 98.6 0.074 14.9 7.3 95656 -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 1.8 1.9 97.4 0.87 2.3 7.3
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 1L6X and 3RJD 1.8 39.7 90855 4800 98.52 0.17497 0.17286 0.1838 0.21501 0.2218 RANDOM 42.262
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] -0.76 0.81 -0.45 0.19
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.416 r_long_range_B_other 8.238 r_scangle_other 7.433 r_scbond_it 5.104 r_scbond_other 5.104 r_mcangle_it 4.79 r_mcangle_other 4.79 r_mcbond_it 3.705 r_mcbond_other 3.687 r_angle_refined_deg 2.134
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.416 r_long_range_B_other 8.238 r_scangle_other 7.433 r_scbond_it 5.104 r_scbond_other 5.104 r_mcangle_it 4.79 r_mcangle_other 4.79 r_mcbond_it 3.705 r_mcbond_other 3.687 r_angle_refined_deg 2.134 r_angle_other_deg 0.921 r_chiral_restr 0.202 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5423 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 374
Software Software Software Name Purpose REFMAC refinement