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Crystal Structure of mouse RANK bound to RANKL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JTZ PDB ENTRY 1JTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 2.0 M sodium chloride, 100 mM EDTA, 100 mM sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 5.2 76.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.636 α = 90 b = 120.636 β = 90 c = 94.297 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 IMAGE PLATE RIGAKU RAXIS IV++ 2005-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.7 20 98.1 0.08 13.9 21055 21040
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 2.7 2.87 92.6 0.537
Refinement Statistics Diffraction ID Structure Solution 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1JTZ 2.7 19.74 21055 21040 1995 97.9 0.191 0.188 0.1904 0.216 0.2181 43.99
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.459 f_angle_d 0.597 f_chiral_restr 0.043 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2475 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 17
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction HKL-2000 data scaling