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Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 1.1-1.25 M tri-sodium citrate, pH 5.5-8, sitting drop, temperature 277K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.84 56.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.837 α = 90 b = 173.725 β = 90 c = 82.574 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315r 2008-01-11 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
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 2.7 54 100 0.121 0.121 6.4 6.1 55240 57
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) 2.7 2.85 100 0.566 0.566 2.7 6.1 7974
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1Q12 2.7 54 55240 2768 0.247 0.2453 0.308 0.3042 RANDOM 59.261
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.56 r_dihedral_angle_3_deg 16.715 r_dihedral_angle_4_deg 14.937 r_dihedral_angle_1_deg 4.674 r_angle_refined_deg 0.948 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11424 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection d*TREK data reduction SCALA data scaling PHASER phasing