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Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with CDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 40 to 44% MPD, 0.1M MOPS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.04 59.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.419 α = 90 b = 154.419 β = 90 c = 187.039 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 mirrors 2007-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.064 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 95.3 99.7 0.077 6 4.7 45481 45481 56.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.53 99.9 0.433 1.7 4.8 6609
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 2.4 20 44357 2366 99.59 0.19635 0.1944 0.1951 0.23347 0.2347 RANDOM 47.789
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] 0.08 -0.12 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 25.698 r_dihedral_angle_3_deg 17.887 r_dihedral_angle_1_deg 6.761 r_scangle_it 3.018 r_scbond_it 1.857 r_angle_refined_deg 1.542 r_mcangle_it 1.309 r_mcbond_it 0.732 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 25.698 r_dihedral_angle_3_deg 17.887 r_dihedral_angle_1_deg 6.761 r_scangle_it 3.018 r_scbond_it 1.857 r_angle_refined_deg 1.542 r_mcangle_it 1.309 r_mcbond_it 0.732 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.1 r_metal_ion_refined 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6312 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 156
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling