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EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 METHOD - HANGING DROP VAPOR DIFFUSION. RESERVOIR: 100 MM MES (PH 5.6) 20% PEG 4000, 500 MM NACL, 10 MM MGCL2, 10 MM DTT PROTEIN: 10MG/ML 1MM HEPES PH 7.2 1M NACL, 10 MM DTT DRY DNA RESUSPENDED IN THE PROTEIN CONTAINING SOLUTION IN MOLAR RATIO 1.5 (DSDNA) / 1.0 (EBNA1 DIMER) DROP: 50% PROTEIN/DNA SOLUTION 50% RESERVOIR SOLUTION CRYSTALLIZATION TEMPERATURE: 4 GEDREES C, vapor diffusion - hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.083 α = 90 b = 64.501 β = 90 c = 111.938 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 CUSTOM-MADE 1994-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 CHESS F1
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 20 98.9 0.073 4.5 5.5 25865 -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) 2.1 2.18 93.2 0.121 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1VHI 2.2 6 2 21158 98.4 0.208 0.208 0.1988 0.268 0.2571 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.5 x_scangle_it 3 x_mcangle_it 2.5 x_scbond_it 2.5 x_mcbond_it 2 x_angle_deg 1.7 x_improper_angle_d 1.5 x_bond_d 0.012 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.5 x_scangle_it 3 x_mcangle_it 2.5 x_scbond_it 2.5 x_mcbond_it 2 x_angle_deg 1.7 x_improper_angle_d 1.5 x_bond_d 0.012 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms 732 Solvent Atoms 182 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building X-PLOR refinement X-PLOR phasing