☰ Navigation Tabs
Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.9 M succinate pH 7, 2% PEG 2000, 0.1 M MES pH 6 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.36 71.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.83 α = 90 b = 182.38 β = 90 c = 232.47 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M mirrors 2013-03-22 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 2.03 Diamond I02 2 Diamond I24
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 2.03 71.75 99.4 0.041 0.041 15.6 4 101947 95399 -3 52.8
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 2.03 2.1 98 0.56 0.56 2.3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.03 71.75 91103 90598 4783 99.4 0.18863 0.18732 0.1846 0.21278 0.2086 RANDOM 52.854
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] -1.09 2.24 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.826 r_dihedral_angle_3_deg 15.569 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_1_deg 5.394 r_angle_refined_deg 1.363 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5929 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 63
Software Software Software Name Purpose EDNA data collection SHELX model building REFMAC refinement XDS data reduction Aimless data scaling SHELX phasing