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Crystal structure of reconstructed bacterial ancestral NDK, Bac1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M SODIUM CACODYLATE, 1.4M SODIUM ACETATE TRIHYDRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.49 64.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.349 α = 90 b = 109.349 β = 90 c = 109.349 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 73 CCD ADSC QUANTUM 315r 2006-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.4 20 100 0.058 59.774 14.6 17316
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 2.4 2.49 100 0.223 14.8
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 MOLECULAR REPLACEMENT THROUGHOUT 2.4 20 17295 877 99.8 0.18 0.178 0.1794 0.221 0.2235 RANDOM 32.793
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 33.265 r_dihedral_angle_4_deg 23.555 r_dihedral_angle_3_deg 17.485 r_scangle_it 6.62 r_dihedral_angle_1_deg 6.491 r_scbond_it 4.008 r_mcangle_it 2.145 r_angle_refined_deg 1.983 r_mcbond_it 1.129 r_chiral_restr 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.265 r_dihedral_angle_4_deg 23.555 r_dihedral_angle_3_deg 17.485 r_scangle_it 6.62 r_dihedral_angle_1_deg 6.491 r_scbond_it 4.008 r_mcangle_it 2.145 r_angle_refined_deg 1.983 r_mcbond_it 1.129 r_chiral_restr 0.149 r_bond_refined_d 0.026 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2190 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling