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Crystal Structure of a T.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6A Complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1M HEPES, 1.0M succinic acid, 1%(w/v) PEG 2000 MME, 4mM Ap6A, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.82 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.413 α = 90 b = 54.775 β = 90 c = 111.673 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 IMAGE PLATE RIGAKU RAXIS VII 2003-11-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418, 0.9744, 0.9792, 0.9798, 0.9819
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 50 99.9 0.032 42.3 22476 3 9.9
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 2.07 100 0.078 23.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 19.96 22254 2212 99.3 0.195 0.195 0.1951 0.225 0.2252 RANDOM 18.2
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] 6.93 -2.46 -4.47
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.02 c_scbond_it 2.03 c_angle_deg 1.9 c_mcangle_it 1.82 c_mcbond_it 1.23 c_improper_angle_d 0.96 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.02 c_scbond_it 2.03 c_angle_deg 1.9 c_mcangle_it 1.82 c_mcbond_it 1.23 c_improper_angle_d 0.96 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 78
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing