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The structure of Ca2+ Sensor (Case-12)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O77 PDB ENTRY 3O77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 Reservoir: 100mM Tris HCL (pH 5.5), 100mM (NH4)2SO4, 21% PEG 3350; Protein stock: 7.6 mg/ml Protein, 50mM Tris HCl (pH 7.4), 150mM NaCl; Seed stock solution: 20mM CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.374 α = 90 b = 101.635 β = 91.45 c = 82.211 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 IMAGE PLATE MAR scanner 345 mm plate 2007-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 100 99.8 0.101 12 3.7 23464 41.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.71 99.8 0.517 2.8 3.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3O77 2.6 50.83 22326 22288 1173 99.83 0.24546 0.24183 0.2605 0.31614 0.3251 RANDOM 22.432
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] -1.01 0.06 0.32 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_3_deg 21.239 r_dihedral_angle_4_deg 20.667 r_dihedral_angle_1_deg 8.346 r_angle_refined_deg 1.726 r_symmetry_hbond_refined 0.372 r_symmetry_vdw_refined 0.328 r_nbtor_refined 0.319 r_nbd_refined 0.268 r_xyhbond_nbd_refined 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_3_deg 21.239 r_dihedral_angle_4_deg 20.667 r_dihedral_angle_1_deg 8.346 r_angle_refined_deg 1.726 r_symmetry_hbond_refined 0.372 r_symmetry_vdw_refined 0.328 r_nbtor_refined 0.319 r_nbd_refined 0.268 r_xyhbond_nbd_refined 0.205 r_metal_ion_refined 0.178 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6338 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 8
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling