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Crystal Structure of MARCKS calmodulin binding domain peptide complexed with Ca2+/Calmodulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QIV PDB ENTRY 1QIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 PEG 6000, sodium acetate, calcium chrolide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.1 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.229 α = 90 b = 40.229 β = 90 c = 343.468 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 IMAGE PLATE RIGAKU RAXIS V 2000-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.02 SPring-8 BL45PX
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 2 200 95.9 0.079 14.2 7.6 12467 11956 31.55
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) 2 2.07 98 0.27 1149
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1QIV 2 20 1 11722 11336 569 96.7 0.22513 0.22308 0.2306 0.26686 0.2665 RANDOM 38.144
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] 0.75 0.37 0.75 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.455 r_scangle_it 5.497 r_scbond_it 3.384 r_dihedral_angle_1_deg 3.101 r_mcangle_it 2.31 r_angle_refined_deg 1.653 r_mcbond_it 1.299 r_angle_other_deg 0.87 r_nbd_refined 0.262 r_nbd_other 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.455 r_scangle_it 5.497 r_scbond_it 3.384 r_dihedral_angle_1_deg 3.101 r_mcangle_it 2.31 r_angle_refined_deg 1.653 r_mcbond_it 1.299 r_angle_other_deg 0.87 r_nbd_refined 0.262 r_nbd_other 0.228 r_symmetry_vdw_other 0.216 r_xyhbond_nbd_refined 0.169 r_metal_ion_refined 0.154 r_symmetry_hbond_refined 0.138 r_symmetry_vdw_refined 0.13 r_chiral_restr 0.1 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbtor_other r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement