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Crystal structure of IP3 3-K calmodulin binding region in complex with Calmodulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAY PDB ENTRY 2VAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 29% W/V POLYETHYLENE GLYCOL 4000, 0.2 M (NH4)2SO4, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0 AND 10 MM SPERMIDINE
Crystal Properties Matthews coefficient Solvent content 4 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.48 α = 90 b = 159.48 β = 90 c = 159.48 γ = 90
Symmetry Space Group I 4 3 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 PIXEL DECTRIS PILATUS 6M KB FOCUSING MIRRORS 2012-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 2.34 79.74 100 0.09 5.91 13.9 14994 2
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 2.34 2.46 100 0.35 2.06 12.66
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 2VAY 2.34 79.65 14144 752 99.96 0.18916 0.18805 0.201 0.21041 0.2204 RANDOM 35.465
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] 5.77 -1.8 -18.88 -11.33 -2.03 5.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.239 r_dihedral_angle_3_deg 17.038 r_dihedral_angle_4_deg 16.743 r_dihedral_angle_1_deg 5.608 r_scbond_it 3.478 r_mcangle_it 3.286 r_mcbond_it 2.104 r_angle_refined_deg 1.451 r_chiral_restr 0.085 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.239 r_dihedral_angle_3_deg 17.038 r_dihedral_angle_4_deg 16.743 r_dihedral_angle_1_deg 5.608 r_scbond_it 3.478 r_mcangle_it 3.286 r_mcbond_it 2.104 r_angle_refined_deg 1.451 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_refined 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 1305 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing