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1.7-A structure of calmodulin bound to a peptide from DAP kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WRZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 295 PEG 8000, sodium acetate, calcium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.07 α = 90 b = 33.71 β = 111.16 c = 75.89 γ = 90
Symmetry Space Group C 1 2 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 CCD MARRESEARCH 2005-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.938 EMBL/DESY, HAMBURG BW7A
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 1.7 20 96.8 0.056 20.1 4.6 16769 16769 -3 -3 28
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 1.7 1.75 94.5 0.52 2.6 3.5 1362
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 (All) 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 1WRZ 1.7 20 -3 16768 16768 846 96.21 0.20286 0.20286 0.19999 0.2147 0.25707 0.2619 RANDOM 9.375
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] 1.65 0.81 -0.87 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.495 r_dihedral_angle_4_deg 18.557 r_dihedral_angle_3_deg 17.418 r_dihedral_angle_1_deg 5.915 r_scangle_it 3.596 r_scbond_it 2.547 r_angle_other_deg 2.026 r_mcangle_it 1.797 r_angle_refined_deg 1.442 r_mcbond_it 1.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.495 r_dihedral_angle_4_deg 18.557 r_dihedral_angle_3_deg 17.418 r_dihedral_angle_1_deg 5.915 r_scangle_it 3.596 r_scbond_it 2.547 r_angle_other_deg 2.026 r_mcangle_it 1.797 r_angle_refined_deg 1.442 r_mcbond_it 1.408 r_symmetry_vdw_other 0.255 r_nbd_refined 0.229 r_nbd_other 0.205 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.173 r_mcbond_other 0.165 r_symmetry_vdw_refined 0.154 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.091 r_nbtor_other 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1320 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing