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Crystal Structure of the CARDB domain of the PF1109 protein in complex with di-metal ions from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR193A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KL6 PDB entry 2KL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch, under oil 5 291 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M sodium acetate (pH 5), 20% PEG 4K, and 0.1M magnesium sulfate, Microbatch, under oil, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.8 31.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.551 α = 90 b = 72.665 β = 93.44 c = 58.456 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 4 mirrors 2009-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97947 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 30 95.8 0.055 0.045 21.1 3.1 44957 43069 9.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 85.2 0.273 0.22 3.34 2.6 4599
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 PDB entry 2KL6 1.7 19.49 2 2 44380 37635 1883 84.8 0.192 0.191 0.19 0.205 0.212 0.2258 RANDOM 21.1
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] -1.79 0.28 7.27 -5.48
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 28.3 c_angle_deg 1.2 c_improper_angle_d 0.73 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1782 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement