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Crystal Structure of the Human Rhesus Glycoprotein RhCG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1M Tris pH 8.5 (at 293K), 40% PEG 200 + 20mM Tris pH 7.4 (at 293K), 100mM NaCl, 40mM BOG, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.83 α = 90 b = 99.83 β = 90 c = 101.076 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 4 2008-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
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 2.1 86.39 99.7 0.077 0.089 39.7 10.6 33464 33449 2
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 2.1 2.18 95.8 0.589 0.637 3.4 8.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3B9W 2.1 86.39 33464 31746 1695 99.68 0.16973 0.16837 0.19505 0.1899 RANDOM 24.109
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] 0.69 0.34 0.69 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.159 r_dihedral_angle_3_deg 12.602 r_dihedral_angle_4_deg 9.676 r_dihedral_angle_1_deg 5.133 r_scangle_it 1.881 r_scbond_it 1.204 r_angle_refined_deg 1.018 r_angle_other_deg 0.87 r_mcangle_it 0.79 r_mcbond_it 0.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.159 r_dihedral_angle_3_deg 12.602 r_dihedral_angle_4_deg 9.676 r_dihedral_angle_1_deg 5.133 r_scangle_it 1.881 r_scbond_it 1.204 r_angle_refined_deg 1.018 r_angle_other_deg 0.87 r_mcangle_it 0.79 r_mcbond_it 0.429 r_mcbond_other 0.095 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3163 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 20
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling