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Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with rhodopsin kinase peptide from Homo sapiens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YOU PDB ENTRY 2YOU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.12M ALCOHOLS (1,6-HEXANEDIOL; 1- BUTANOL;1,PROPANEDIOL(RACEMIC); 2-PROPONOL; 1, 4-BUTANEDIOL; 1,3- PROPANEDIOL); 0.1M BUFFER 2 (SODIUM HEPES; MOPS ACID PH 7.5); P550MME_P20K 30%.
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.69 α = 90 b = 93.69 β = 92.25 c = 55.71 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 100 2014-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.3 48 99.2 0.04 15.8 3.3 18488 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 2.3 2.36 94.3 0.37 2.2 2.6
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 2YOU 2.3 47.86 17512 956 99.16 0.22708 0.22556 0.2278 0.25515 0.2621 RANDOM 46.458
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] 0.74 -0.34 -0.36 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.02 r_dihedral_angle_4_deg 14.574 r_dihedral_angle_3_deg 14.328 r_dihedral_angle_1_deg 4.913 r_mcangle_it 2.452 r_scbond_it 2.387 r_mcbond_it 1.689 r_mcbond_other 1.682 r_angle_refined_deg 1.238 r_angle_other_deg 0.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.02 r_dihedral_angle_4_deg 14.574 r_dihedral_angle_3_deg 14.328 r_dihedral_angle_1_deg 4.913 r_mcangle_it 2.452 r_scbond_it 2.387 r_mcbond_it 1.689 r_mcbond_other 1.682 r_angle_refined_deg 1.238 r_angle_other_deg 0.738 r_chiral_restr 0.076 r_gen_planes_refined 0.005 r_bond_refined_d 0.002 r_gen_planes_other 0.002 r_bond_other_d 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_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 2988 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing