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Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2 M tartrate Na/K, 0.1 M MES (pH 6.5) and 20% PEG 2K, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.43 α = 90 b = 39.49 β = 109.31 c = 94.2 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 4 2007-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.6064 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 88.891 97.2 0.076 0.076 0.105 0.056 13.3 3.5 30472 30472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 94.6 0.426 0.426 0.61 0.32 1.7 3.5 4280
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 MOLECULAR REPLACEMENT THROUGHOUT 2 44.46 30458 1538 97.15 0.193 0.19 0.1987 0.254 0.262 RANDOM 25.163
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] -0.01 -0.02 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.994 r_dihedral_angle_4_deg 20.444 r_dihedral_angle_3_deg 16.778 r_dihedral_angle_1_deg 6.069 r_scangle_it 5.078 r_scbond_it 3.23 r_angle_refined_deg 1.902 r_mcangle_it 1.677 r_mcbond_it 0.985 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.994 r_dihedral_angle_4_deg 20.444 r_dihedral_angle_3_deg 16.778 r_dihedral_angle_1_deg 6.069 r_scangle_it 5.078 r_scbond_it 3.23 r_angle_refined_deg 1.902 r_mcangle_it 1.677 r_mcbond_it 0.985 r_chiral_restr 0.141 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3397 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 22
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection