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Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YI9 PDB ENTRY 2YI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP CRYSTALS OF FULL-LENGTH VP1 WERE GROWN IN SITTING DROPS CONTAINING 100 NL PROTEIN (5.3 MG/ML) PLUS 5 MM MNCL2 AND 100 NL RESERVOIR SOLUTION (20% W/V PEG3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0.2 M SODIUM CITRATE, 20 MM ATP, 5% V/V MPD, 10 MM NAOH) EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20.5 C.
Crystal Properties Matthews coefficient Solvent content 3.02 63.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.74 α = 90 b = 195.45 β = 90 c = 197.38 γ = 90
Symmetry Space Group P 21 21 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 4r 2006-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 3.8 45.24 98.5 0.3 4.5 4.9 45508 -3 51.01
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 3.8 4.01 99 0.82 1.8 4.7
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 2YI9 3.8 44.43 45473 2307 0.1858 0.1843 0.2029 0.2129 0.2294 RANDOM 99.51
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] 1.9344 6.3521 -8.2865
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.68 t_omega_torsion 2.49 t_angle_deg 1.08 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.68 t_omega_torsion 2.49 t_angle_deg 1.08 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24183 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement MOSFLM data reduction SCALA data scaling PHASER phasing