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Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I8F PDB entry 1I8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 293 sodium acetate, ammonium acetate, PEG 4000, glycerol,
uridine-5'-monophosphate, dithiothreitol, pH 8.2, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.829 α = 90 b = 113.764 β = 90 c = 126.594 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 Osmic mirrors 2001-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 2.05 100 97.4 0.115 17.9 8.1 40722 40722 -1.73 -3 14.3
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 2.05 2.12 95.5 0.509 4.1 3949
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 PDB entry 1I8F 2.05 19.78 39951 39951 2005 95.5 0.182 0.182 0.182 0.1755 0.226 0.2176 RANDOM 28.1
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] 1.94 5.68 -7.62
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_scangle_it 3.71 c_scbond_it 2.66 c_mcangle_it 2.13 c_angle_deg 1.6 c_mcbond_it 1.53 c_improper_angle_d 1 c_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4007 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 187
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing CNS refinement