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Crystal structures of Iron containing Adenylate kinase from Desulfovibrio gigas
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 277 0.2M tartrate Na/K, 0.1M MES (pH 6.5), 20% PEG 2000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.45 64.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.8 α = 90 b = 119.16 β = 90 c = 146.71 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 CCD ADSC QUANTUM 4 2008-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 1.7266 ESRF ID14-2
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 3 92.495 91.3 0.078 0.078 0.099 0.048 15 3.9 6444 6444
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 3 3.17 92 0.246 0.246 0.32 0.16 2.4 4 918
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 3 46.25 6444 297 90.14 0.189 0.186 0.187 0.252 0.2531 RANDOM 40.265
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] -1.4 -0.35 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.509 r_dihedral_angle_3_deg 20.453 r_dihedral_angle_4_deg 11.388 r_dihedral_angle_1_deg 7.011 r_scangle_it 3.55 r_scbond_it 2.061 r_angle_refined_deg 1.817 r_mcangle_it 1.169 r_mcbond_it 0.584 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.509 r_dihedral_angle_3_deg 20.453 r_dihedral_angle_4_deg 11.388 r_dihedral_angle_1_deg 7.011 r_scangle_it 3.55 r_scbond_it 2.061 r_angle_refined_deg 1.817 r_mcangle_it 1.169 r_mcbond_it 0.584 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1668 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 7
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling DM phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection PHASER phasing