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Crystal Structure of NTB-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 0.4-0.5 M CaCl2, 0.1 M HEPES pH 7.4, 1.0 mM Pt(NH3)2Cl2, 4% PEG-400, Vapor diffusion, Sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.13 70.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.196 α = 90 b = 148.452 β = 112.86 c = 86.572 γ = 90
Symmetry Space Group C 1 2 1
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 2005-10-20 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9789,0.9791,0.9714 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 40 99.7 0.059 0.048 15.1 3.2 28402 28402 51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 99.9 0.348 0.303 3.08 3.2 2838
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 3 40 28151 28151 1413 99.67 0.216 0.216 0.213 0.2081 0.266 0.2602 RANDOM 83.603
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] 2.85 3.14 -1.44 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_dihedral_angle_3_deg 19.258 r_dihedral_angle_4_deg 15.413 r_dihedral_angle_1_deg 6.209 r_scangle_it 4.239 r_scbond_it 2.517 r_mcangle_it 1.793 r_angle_refined_deg 1.085 r_mcbond_it 1.004 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_dihedral_angle_3_deg 19.258 r_dihedral_angle_4_deg 15.413 r_dihedral_angle_1_deg 6.209 r_scangle_it 4.239 r_scbond_it 2.517 r_mcangle_it 1.793 r_angle_refined_deg 1.085 r_mcbond_it 1.004 r_nbtor_refined 0.332 r_nbd_refined 0.299 r_symmetry_vdw_refined 0.293 r_symmetry_metal_ion_refined 0.239 r_xyhbond_nbd_refined 0.207 r_metal_ion_refined 0.164 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5960 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing Coot model building O model building