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Crystal structure of the N-terminal region of the human ryanodine receptor 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XOA PDB entry 2XOA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 20 mM TRIS-HCl, 150 mM NaCl, 10% glycerol, 7mM mercaptoethanol, 1 mM CHAPS, 0.1% betaine, 100 mM HEPES, 200 mM ammonium formate, 21% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.45 α = 90 b = 75.45 β = 90 c = 248.84 γ = 90
Symmetry Space Group P 42 21 2
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 2012-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
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 2.39 124.42 100 0.16 0.15 12.2 13.8 29469 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.52 95
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 PDB entry 2XOA 2.39 44.77 27960 1444 99.35 0.2258 0.22405 0.2232 0.26087 0.2579 RANDOM 62.542
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] 1.84 1.84 -3.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 74.934 r_dihedral_angle_2_deg 37.941 r_sphericity_bonded 26.956 r_dihedral_angle_3_deg 15.959 r_dihedral_angle_4_deg 15.943 r_dihedral_angle_1_deg 5.908 r_rigid_bond_restr 3.886 r_angle_refined_deg 1.185 r_chiral_restr 0.082 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 74.934 r_dihedral_angle_2_deg 37.941 r_sphericity_bonded 26.956 r_dihedral_angle_3_deg 15.959 r_dihedral_angle_4_deg 15.943 r_dihedral_angle_1_deg 5.908 r_rigid_bond_restr 3.886 r_angle_refined_deg 1.185 r_chiral_restr 0.082 r_bond_refined_d 0.008 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3934 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling