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Crystal Structure of diiron adenine deaminase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NQB PDB entry 3NQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2M Magnesium chloride hexahydrate, 0.1M HEPES 7.5, 25% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.662 α = 90 b = 131.845 β = 97.04 c = 69.628 γ = 90
Symmetry Space Group P 1 21 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 mirrors 2010-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979 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 2.63 50 99.6 0.1 7.2 7.5 32849 32849
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 2.63 2.68 93.9 0.78 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Difference Fourier THROUGHOUT PDB entry 3NQB 2.63 48.89 31122 31123 1663 99.64 0.19025 0.18501 0.1856 0.28726 0.2845 RANDOM 51.47
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] -0.01 -0.02 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.319 r_dihedral_angle_4_deg 21.843 r_dihedral_angle_3_deg 21.722 r_dihedral_angle_1_deg 10.382 r_scangle_it 6.696 r_scbond_it 4.821 r_angle_refined_deg 3.225 r_mcangle_it 2.606 r_mcbond_it 1.838 r_nbtor_refined 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.319 r_dihedral_angle_4_deg 21.843 r_dihedral_angle_3_deg 21.722 r_dihedral_angle_1_deg 10.382 r_scangle_it 6.696 r_scbond_it 4.821 r_angle_refined_deg 3.225 r_mcangle_it 2.606 r_mcbond_it 1.838 r_nbtor_refined 0.347 r_nbd_refined 0.287 r_symmetry_vdw_refined 0.267 r_metal_ion_refined 0.219 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.197 r_symmetry_hbond_refined 0.102 r_bond_refined_d 0.042 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8614 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 6
Software Software Software Name Purpose CBASS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing