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Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium-binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Se-Met structure of CabD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG 8000, Cacodylate Sodium, Zinc Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.876 α = 90 b = 51.044 β = 90 c = 86.998 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2007-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.8 50 98.9 0.054 11.9 4.3 21409 -3
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) 1.8 1.91 94.6 0.337 2.8 3.5 1683
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 (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 Se-Met structure of CabD 1.8 25.22 13404 13404 734 99.77 0.209 0.19926 0.19671 0.1966 0.24826 0.2507 RANDOM 20.116
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] -0.18 -0.77 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.948 r_dihedral_angle_4_deg 18.035 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_1_deg 4.753 r_scangle_it 3.391 r_scbond_it 2.234 r_angle_refined_deg 1.336 r_mcangle_it 1.26 r_mcbond_it 0.844 r_symmetry_metal_ion_refined 0.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.948 r_dihedral_angle_4_deg 18.035 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_1_deg 4.753 r_scangle_it 3.391 r_scbond_it 2.234 r_angle_refined_deg 1.336 r_mcangle_it 1.26 r_mcbond_it 0.844 r_symmetry_metal_ion_refined 0.521 r_symmetry_vdw_refined 0.462 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.297 r_metal_ion_refined 0.272 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1224 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 9
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling