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Crystal structure of a putative cyclic nucleotide binding protein (spoa0323) from ruegeria pomeroyi dss-3 at 2.35 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 1.2600M (NH4)2SO4, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.052 α = 90 b = 137.052 β = 90 c = 94.937 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-01-19 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2008-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2 2 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97967,0.94645 APS 23-ID-B
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 2.35 28.724 98.2 0.047 11.09 3.82 27604 -3 56.796
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) 2.35 2.43 96 0.603 1.4
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 2.35 28.724 27596 1409 99.83 0.204 0.202 0.2111 0.236 0.2444 RANDOM 71.309
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] -0.62 -0.31 -0.62 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.134 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 12.223 r_scangle_it 8.009 r_scbond_it 6.013 r_dihedral_angle_1_deg 3.534 r_mcangle_it 3.417 r_mcbond_it 2.094 r_angle_refined_deg 1.725 r_angle_other_deg 1.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.134 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 12.223 r_scangle_it 8.009 r_scbond_it 6.013 r_dihedral_angle_1_deg 3.534 r_mcangle_it 3.417 r_mcbond_it 2.094 r_angle_refined_deg 1.725 r_angle_other_deg 1.055 r_mcbond_other 0.685 r_symmetry_vdw_other 0.317 r_nbd_refined 0.214 r_nbtor_refined 0.18 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.158 r_symmetry_vdw_refined 0.135 r_nbtor_other 0.094 r_chiral_restr 0.064 r_bond_refined_d 0.018 r_xyhbond_nbd_other 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3391 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing