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crystal structure of FBF-2 in complex with gld-1 FBEa13 RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K5Y PDB ENTRY 3K5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 10% [w/v] polyethylene glycol 6000, 5% [v/v] (+/-)-2-methyl-2,4-pentanediol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.04 59.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.465 α = 90 b = 98.465 β = 90 c = 107.982 γ = 120
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 RIGAKU SATURN 92 2009-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.3 24.011 99.85 0.094 0.094 17.7 5.5 26550 26381 2 2 34.488
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 2.3 2.34 100 0.65 0.65 2.3 4.5 1318
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-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 3K5Y 2.3 24.01 2 2 26550 26381 1361 99.9 0.177 0.171 0.2267 0.2218 5%, R-free flags copied from mtz file of 3K5Y 39.7285
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] -0.744 -0.744 1.482
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.324 f_angle_deg 0.74 f_improper_angle_d 0.067 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms 232 Solvent Atoms 318 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling