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Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus, complexed with Ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DG0 PDB ENTRY 2DG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1M HEPES, 1M succinic acid, 1% PEG MME2000, 5mM CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.527 α = 90 b = 181.978 β = 115.41 c = 81.803 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 CCD ADSC QUANTUM 210 2005-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.9 SPring-8 BL44B2
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 1.72 50 99.2 0.063 3.8 211193 15.3
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 1.72 1.78 95 0.395 3.4 20225
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 2DG0 1.72 19.99 211106 20975 99 0.169 0.169 0.1684 0.197 0.1968 RANDOM 18.8
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] 1.19 2.33 -4.4 3.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26 c_scangle_it 2.31 c_scbond_it 1.62 c_mcangle_it 1.47 c_angle_deg 1.4 c_mcbond_it 0.99 c_improper_angle_d 0.79 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26 c_scangle_it 2.31 c_scbond_it 1.62 c_mcangle_it 1.47 c_angle_deg 1.4 c_mcbond_it 0.99 c_improper_angle_d 0.79 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15076 Nucleic Acid Atoms Solvent Atoms 2141 Heterogen Atoms 84
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing