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CRYSTAL STRUCTURE OF Z-DNA WITH UNTYPICALLY COORDINATED CA2+ ION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.6 UL 0.4 MM D(CGCGCG)2 SOLUTION MIXED WITH 1.2UL OF THE PRECIPITANT SOLUTION CONSISTING OF 10 MM CACL2, 40 MM NA CACODYLATE PH 6.0, 10% MPD, EQUILIBRATED AGAINST THE WELL SOLUTION OF 35 % MPD, 6 MM SPERMIDINE
Crystal Properties Matthews coefficient Solvent content 1.5 17.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.76 α = 90 b = 28.82 β = 90 c = 42.36 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 RAYONIX MX300-HS 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.992 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.45 24 98.2 0.086 0.096 0.041 15.5 5.5 4084
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 87.9 0.482 0.577 0.308 0.794 1.6 2.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3P4J 1.45 24 4083 209 98.15 0.121 0.121 0.1299 0.172 0.1759 18.8
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] -0.62 -0.18 0.8
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.223 r_rigid_bond_restr 11.541 r_sphericity_bonded 11.421 r_angle_other_deg 8.193 r_scangle_other 4.251 r_scbond_other 3.67 r_scbond_it 3.656 r_long_range_B_refined 3.476 r_long_range_B_other 3.386 r_angle_refined_deg 1.61
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.223 r_rigid_bond_restr 11.541 r_sphericity_bonded 11.421 r_angle_other_deg 8.193 r_scangle_other 4.251 r_scbond_other 3.67 r_scbond_it 3.656 r_long_range_B_refined 3.476 r_long_range_B_other 3.386 r_angle_refined_deg 1.61 r_chiral_restr 0.092 r_gen_planes_other 0.027 r_gen_planes_refined 0.026 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 240 Solvent Atoms 34 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing