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KSHV LANA (ORF73) C-terminal domain, spiral: hexagonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YPY PDB ENTRY 2YPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.4 UL OF 31.5 MG/ML PROTEIN IN 5 MM BISTRIS-CL, 5 MM DTT, PH 6.5 WERE AS SUCH EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 170 MM LITHIUM ACETATE AND 18% (W/V) PEG3350 IN A SITTING DROP SETUP AT 20 DEGREE CENTIGRADE. AFTER TWO DAYS, CRYSTALS WERE DETACHED FROM THE CARRIER PLASTIC BY ADDING 1 UL OF 2 M AMMONIUM FORMATE.
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.18 α = 90 b = 103.18 β = 90 c = 228.25 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2014-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 3.7 89.36 95.9 0.23 18.53 29.7 7874 2 119.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.7 3.84 99.1 1.92 31.3
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 2YPY 3.7 89.36 7485 389 95.83 0.20278 0.20078 0.2067 0.2386 0.2345 RANDOM 115.815
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 -1 -2 6.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.5 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_4_deg 12.955 r_mcangle_it 12.583 r_mcbond_it 7.888 r_mcbond_other 7.885 r_scbond_it 7.588 r_dihedral_angle_1_deg 3.332 r_angle_refined_deg 0.508 r_angle_other_deg 0.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.5 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_4_deg 12.955 r_mcangle_it 12.583 r_mcbond_it 7.888 r_mcbond_other 7.885 r_scbond_it 7.588 r_dihedral_angle_1_deg 3.332 r_angle_refined_deg 0.508 r_angle_other_deg 0.492 r_chiral_restr 0.035 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4316 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing