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Crystal structure of hRANKL-mRANK complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ME2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 0.1 M sodium di-hydrogen phosphate, 2 M sodium chloride, 0.1 M potassium di-hydrogen phosphate and 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 4.84 74.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.188 α = 90 b = 122.188 β = 90 c = 94.473 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 100 CCD MARMOSAIC 225 mm CCD 2008-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 2.8 30 99.8 0.197 14.6 12.1 19916 -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 2.8 2.9 98.2 0.818 2.1 5.7
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 3ME2 2.8 29.37 18885 1018 99.46 0.17246 0.17085 0.171 0.20292 0.2036 RANDOM 56.656
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] 0.35 0.35 0.35 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.218 r_dihedral_angle_4_deg 21.403 r_dihedral_angle_3_deg 14.765 r_long_range_B_refined 8.874 r_dihedral_angle_1_deg 5.759 r_mcangle_it 4.859 r_scbond_it 4.748 r_mcbond_it 3.081 r_angle_refined_deg 1.303 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.218 r_dihedral_angle_4_deg 21.403 r_dihedral_angle_3_deg 14.765 r_long_range_B_refined 8.874 r_dihedral_angle_1_deg 5.759 r_mcangle_it 4.859 r_scbond_it 4.748 r_mcbond_it 3.081 r_angle_refined_deg 1.303 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 2505 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing