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Crystal structure of the calcium chelating immunodominant antigen, calcium dodecin (Rv0379),from Mycobacterium tuberculosis with a novel calcium-binding site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapor diffusion,hanging and sitting drops 8 291 1M Sodium Formate, 10mM CaCl2, pH 8.0, vapor diffusion,hanging and sitting drops, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.17 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.193 α = 90 b = 78.446 β = 90 c = 152.489 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 CCD M MAD 2 1 x-ray M SINGLE WAVELENGTH 3 1 4 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 1.071, 1.072, 1.100 APS 14-BM-D 2 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C 3 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID 4 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 1,2 1.8 76.7 0.027 20.8 1.9 78271
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.8 28.88 78271 3927 99.08 0.1835 0.1812 0.2025 0.2293 0.2483 RANDOM 30.704
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] 0.47 -0.93 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.553 r_dihedral_angle_4_deg 17.195 r_dihedral_angle_3_deg 16.172 r_scangle_it 6.599 r_dihedral_angle_1_deg 6.399 r_scbond_it 4.061 r_mcangle_it 2.212 r_angle_refined_deg 2.062 r_mcbond_it 1.306 r_chiral_restr 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.553 r_dihedral_angle_4_deg 17.195 r_dihedral_angle_3_deg 16.172 r_scangle_it 6.599 r_dihedral_angle_1_deg 6.399 r_scbond_it 4.061 r_mcangle_it 2.212 r_angle_refined_deg 2.062 r_mcbond_it 1.306 r_chiral_restr 0.169 r_bond_refined_d 0.025 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6402 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling SHARP phasing