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Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B8Q PDB ENTRY 1B8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 40-45% MPD, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.839 α = 90 b = 152.528 β = 90 c = 184.12 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 100 CCD ADSC QUANTUM 315 mirrors 2007-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.98025 ESRF BM30A
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 76 98.6 0.06 0.06 7.3 4.7 72791 31.9
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) 2 2.11 98.7 0.303 0.303 2.6 4.8 10642
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1B8Q 2 20 70883 3757 98.28 0.20058 0.19907 0.2009 0.22894 0.2286 RANDOM 33.532
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.467 r_dihedral_angle_4_deg 20.477 r_dihedral_angle_3_deg 15.23 r_dihedral_angle_1_deg 5.999 r_scangle_it 2.836 r_scbond_it 1.673 r_angle_refined_deg 1.305 r_mcangle_it 1.223 r_mcbond_it 0.699 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.467 r_dihedral_angle_4_deg 20.477 r_dihedral_angle_3_deg 15.23 r_dihedral_angle_1_deg 5.999 r_scangle_it 2.836 r_scbond_it 1.673 r_angle_refined_deg 1.305 r_mcangle_it 1.223 r_mcbond_it 0.699 r_nbtor_refined 0.304 r_metal_ion_refined 0.221 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6303 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing