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High-resolution crystal structure of Z-DNA in complex with Cr3+ cations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HIF PDB ENTRY 4HIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 A 1.5 MM WATER SOLUTION OF DNA MIXED
1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 12 MM NACL, 80 MM KCL
AND EQUILIBRATED AGAINST 35% MPD, PH 6. FOR CR3+ SOAKING, THE CRYSTAL WAS
PLACED FOR SEVERAL DAYS IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML
OF 5 MM [CR(H2O)6]CL3, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal Properties Matthews coefficient Solvent content 1.66 24.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 18.14 α = 90 b = 30.44 β = 90 c = 42.94 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 MX-225 2011-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 0.97 24.83 98.4 0.016 24.85 2.53 26535 26535 -3 13.586
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 0.973 1 93.2 0.432 2.05 2.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 4HIF 0.97 24.83 26535 1858 98.4 0.1447 0.1438 0.1438 0.1849 0.1587 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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 13 136 280.78
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.096 s_similar_adp_cmpnt 0.065 s_from_restr_planes 0.0378 s_anti_bump_dis_restr 0.029 s_angle_d 0.028 s_bond_d 0.019 s_rigid_bond_adp_cmpnt 0.009 s_similar_dist s_zero_chiral_vol s_non_zero_chiral_vol
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 240 Solvent Atoms 67 Heterogen Atoms 3
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing SHELXL-97 refinement XDS data reduction XSCALE data scaling