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X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 273 MPD 40 to 44%, MOPS 0.1M, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.9 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.472 α = 90 b = 152.726 β = 90 c = 184.94 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 2007-07-23 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 2.3 92.4 99.7 0.071 6 5 49557 47.885
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) 2.3 2.42 100 0.331 2.3 5.1 7285
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 (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 2b8q 2.3 20 48109 48109 2570 99.62 0.18997 0.18814 0.1902 0.22437 0.2232 RANDOM 42.298
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 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.054 r_dihedral_angle_4_deg 24.046 r_dihedral_angle_3_deg 17.528 r_dihedral_angle_1_deg 6.398 r_scangle_it 3.293 r_scbond_it 1.965 r_angle_refined_deg 1.396 r_mcangle_it 1.315 r_mcbond_it 0.723 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.054 r_dihedral_angle_4_deg 24.046 r_dihedral_angle_3_deg 17.528 r_dihedral_angle_1_deg 6.398 r_scangle_it 3.293 r_scbond_it 1.965 r_angle_refined_deg 1.396 r_mcangle_it 1.315 r_mcbond_it 0.723 r_nbtor_refined 0.304 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6338 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 156
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling