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Crystal structure of the aptamer minF-lysozyme complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M4O PDB ENTRY 4M4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 1.1M Malonic Acid, 0.15 M Ammonium Citrate
Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M
Sodium Formate, 0.096 M Ammonium Tartrate
Dibasic, Final pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.78 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.914 α = 118.59 b = 132.289 β = 96.39 c = 131.539 γ = 96.27
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 315 2013-01-18 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 2.68 50 94.9 0.067 12.1 1.9 67209
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 2.7 2.75 90.9 0.629 1.8
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 4M4O 2.68 38.04 53394 3007 79.53 0.16832 0.16549 0.1723 0.216 0.2119 RANDOM 122.84
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] -33.08 -1.5 -4.37 74.15 -12.52 -41.07
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 53.84 r_dihedral_angle_2_deg 38.809 r_dihedral_angle_3_deg 18.936 r_dihedral_angle_4_deg 18.677 r_rigid_bond_restr 8.222 r_dihedral_angle_1_deg 7.51 r_mcangle_it 3.878 r_mcbond_it 2.263 r_scbond_it 1.995 r_angle_refined_deg 1.421
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 53.84 r_dihedral_angle_2_deg 38.809 r_dihedral_angle_3_deg 18.936 r_dihedral_angle_4_deg 18.677 r_rigid_bond_restr 8.222 r_dihedral_angle_1_deg 7.51 r_mcangle_it 3.878 r_mcbond_it 2.263 r_scbond_it 1.995 r_angle_refined_deg 1.421 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6006 Nucleic Acid Atoms 5357 Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction