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Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MCW
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 buffer pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.38 71.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.19 α = 90 b = 183.01 β = 90 c = 233.46 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 DECTRIS PILATUS 2M mirror 2013-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 Diamond I04-1
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 2.68 66 99.4 0.077 14.3 4.1 44989 42290 -3 45.2
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 2.68 2.75 99.6 0.68 1.9
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 4MCW 2.68 65.54 42290 40177 2107 98.9 0.186 0.18594 0.18369 0.1868 0.2278 0.2285 RANDOM 60.842
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] -1.29 3.14 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.467 r_dihedral_angle_4_deg 20.72 r_dihedral_angle_3_deg 18.317 r_dihedral_angle_1_deg 6.037 r_angle_refined_deg 1.717 r_chiral_restr 0.112 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5929 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 90
Software Software Software Name Purpose EDNA data collection MOLREP phasing REFMAC refinement XDS data reduction Aimless data scaling