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Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with GDP
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 7.5 293 40-45% 2-Methyl-2,4-pentane-d12-diol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.07 α = 90 b = 70.07 β = 90 c = 103.221 γ = 120
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 210 mirrors 2007-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 60 100 0.117 3.6 7.1 22639 18.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 100 0.35 1.9 5.3 3288
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 2B8Q 1.9 30 21485 1159 99.99 0.18297 0.18122 0.1825 0.21563 0.2132 RANDOM 19.347
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] -0.13 -0.07 -0.13 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.809 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 5.786 r_scangle_it 2.179 r_scbond_it 1.294 r_angle_refined_deg 1.154 r_mcangle_it 0.826 r_mcbond_it 0.48 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.809 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 5.786 r_scangle_it 2.179 r_scbond_it 1.294 r_angle_refined_deg 1.154 r_mcangle_it 0.826 r_mcbond_it 0.48 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.195 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2112 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing