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Crystal structure of mouse RANKL-RANK complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 0.1M sodium di-hydrogen phosphate, 2M sodium chloride, 0.1M potassium di-hydrogen phosphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 4.68 73.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.225 α = 90 b = 121.225 β = 90 c = 94.995 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 ADSC QUANTUM 315 2007-07-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4 2 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 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 2.8 30 100 0.191 18.6 16.3 18587 -1
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) 2.8 2.9 100 0.995 2.9 13.8 1970
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 1JTZ 2.8 30 17956 995 99.74 0.17541 0.17388 0.1783 0.20504 0.169 RANDOM 58.14
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] 2.21 1.1 2.21 -3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 19.316 r_dihedral_angle_3_deg 13.798 r_dihedral_angle_1_deg 5.741 r_scangle_it 3.691 r_scbond_it 2.353 r_mcangle_it 2.271 r_mcbond_it 1.203 r_angle_refined_deg 0.999 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 19.316 r_dihedral_angle_3_deg 13.798 r_dihedral_angle_1_deg 5.741 r_scangle_it 3.691 r_scbond_it 2.353 r_mcangle_it 2.271 r_mcbond_it 1.203 r_angle_refined_deg 0.999 r_chiral_restr 0.065 r_bond_refined_d 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2494 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 5
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling