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Crystal structure of the virion-associated protein P3 from caulimovirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F6N PDB ENTRY 3F6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 291 25% PEG 1000, 0.1M MES-NAOH BUFFER, 1.2 MOLAR-EXCESS DNA OLIGONUCLEOTIDE (POLY-AT, 14 BP) , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.81 31.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.302 α = 90 b = 28.818 β = 92.08 c = 75.957 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2009-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.59 18.98 96.1 0.074 0.084 14.4 4.3 9317 60.1
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 2.59 2.74 99.2 0.302 0.345 3.6 4.4
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 PDB ENTRY 3F6N 2.59 18.98 9317 8660 657 96.1 0.223 0.219 0.2443 0.289 0.3058 RANDOM 25.07
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 -0.08 -0.07 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.551 r_dihedral_angle_3_deg 20.609 r_dihedral_angle_1_deg 5.391 r_scangle_it 2.187 r_scbond_it 1.274 r_angle_refined_deg 1.255 r_mcangle_it 0.722 r_mcbond_it 0.373 r_chiral_restr 0.085 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.551 r_dihedral_angle_3_deg 20.609 r_dihedral_angle_1_deg 5.391 r_scangle_it 2.187 r_scbond_it 1.274 r_angle_refined_deg 1.255 r_mcangle_it 0.722 r_mcbond_it 0.373 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2153 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling