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Structure and interactions of the RNA-dependent RNA polymerase from bacteriophage phi12 (P1 crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GZK PDB ENTRY 4GZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2 M Mg formate
20% PEG 3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.874 α = 75.16 b = 94.47 β = 63.11 c = 96.481 γ = 83.79
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 MAR CCD 165 mm 2012-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 2.1 50 92.6 0.048 17.8 1.9 156487 144893 -3
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 2.1 2.14 87.1 0.202 2.9 1.7 7802
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 (All) 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 4GZK 2.1 50 156991 137611 7276 92.29 0.22 0.22025 0.2172 0.2241 0.27836 0.2867 RANDOM 27.467
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] -0.1 0.62 -0.17 0.57 -0.53 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 13.926 r_dihedral_angle_1_deg 5.646 r_scangle_it 1.818 r_scbond_it 1.112 r_angle_refined_deg 1.1 r_angle_other_deg 0.817 r_mcangle_it 0.685 r_mcbond_it 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 13.926 r_dihedral_angle_1_deg 5.646 r_scangle_it 1.818 r_scbond_it 1.112 r_angle_refined_deg 1.1 r_angle_other_deg 0.817 r_mcangle_it 0.685 r_mcbond_it 0.366 r_mcbond_other 0.074 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20846 Nucleic Acid Atoms Solvent Atoms 1655 Heterogen Atoms 4
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling