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The thermo- and acido-stable ORF-99 from the archaeal virus AFV1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DF6 PDB ENTRY 3DF6 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.35M Sodium Citrate, 0.1M Sodium Hepes, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.23 61.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.411 α = 90 b = 101.411 β = 90 c = 58.522 γ = 90
Symmetry Space Group P 41 21 2
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 210 2006-08-25 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) 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 3.1 40 99.7 0.101 0.101 4.4 7.5 5897 84.6
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) 1 3.1 3.27 100 0.556 0.556 3.3 7.8 843
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 3DF6 chain A 3.1 15 5246 560 99.66 0.24976 0.24504 0.2585 0.29631 0.2942 RANDOM 66.857
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] -2.77 -2.77 5.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.124 r_dihedral_angle_3_deg 18.415 r_dihedral_angle_4_deg 12.848 r_dihedral_angle_1_deg 5.505 r_angle_refined_deg 1.065 r_scangle_it 0.935 r_scbond_it 0.564 r_nbtor_refined 0.308 r_mcangle_it 0.279 r_symmetry_vdw_refined 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.124 r_dihedral_angle_3_deg 18.415 r_dihedral_angle_4_deg 12.848 r_dihedral_angle_1_deg 5.505 r_angle_refined_deg 1.065 r_scangle_it 0.935 r_scbond_it 0.564 r_nbtor_refined 0.308 r_mcangle_it 0.279 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.17 r_mcbond_it 0.146 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1582 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing