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Crystal structure of BA2930 in complex with AcCoA and cytosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KZL PDB entry 3KZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES-Na, 0.18M MgCl2,
15% w/v PEG3350, 2% w/v CHAPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.473 α = 90 b = 110.63 β = 112.24 c = 73.78 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 MARMOSAIC 300 mm CCD beryllium lenses 2010-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 50 97.2 0.094 0.094 15.7 3 70634 70634 -3
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 2 2.03 99 0.418 0.418 2.6 3 3593
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 (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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3KZL 2 23.99 66906 66906 3546 96.98 0.17712 0.17712 0.17431 0.187 0.22957 0.2396 RANDOM 27.617
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] -0.17 -0.15 -0.14 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.465 r_dihedral_angle_4_deg 17.888 r_dihedral_angle_3_deg 14.979 r_dihedral_angle_1_deg 6.149 r_scangle_it 3.581 r_scbond_it 2.369 r_angle_refined_deg 1.48 r_mcangle_it 1.273 r_angle_other_deg 0.962 r_mcbond_it 0.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.465 r_dihedral_angle_4_deg 17.888 r_dihedral_angle_3_deg 14.979 r_dihedral_angle_1_deg 6.149 r_scangle_it 3.581 r_scbond_it 2.369 r_angle_refined_deg 1.48 r_mcangle_it 1.273 r_angle_other_deg 0.962 r_mcbond_it 0.685 r_mcbond_other 0.177 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8242 Nucleic Acid Atoms Solvent Atoms 670 Heterogen Atoms 297
Software Software Software Name Purpose MD2 data collection HKL-3000 phasing MOLREP phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling