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Crystal structure of reconstructed archaeal ancestral NDK, Arc1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES, 0.8M POTTASIUM SODIUM TARTRATE TETRAHYDRATE, 3% 2-METHYL-2,4,-PENTADIOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.58 65.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.398 α = 90 b = 110.398 β = 90 c = 110.398 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 2007-01-17 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 99.8 0.071 38.379 10.2 17715
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 98.1 0.539 5.8
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-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 2cwk 2.4 19.52 17682 900 99.8 0.187 0.186 0.1806 0.222 0.2169 RANDOM 49.28
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 36.123 r_dihedral_angle_4_deg 21.454 r_dihedral_angle_3_deg 18.349 r_scangle_it 6.991 r_dihedral_angle_1_deg 6.774 r_scbond_it 4.199 r_mcangle_it 2.178 r_angle_refined_deg 1.986 r_mcbond_it 1.135 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.123 r_dihedral_angle_4_deg 21.454 r_dihedral_angle_3_deg 18.349 r_scangle_it 6.991 r_dihedral_angle_1_deg 6.774 r_scbond_it 4.199 r_mcangle_it 2.178 r_angle_refined_deg 1.986 r_mcbond_it 1.135 r_chiral_restr 0.158 r_bond_refined_d 0.025 r_gen_planes_refined 0.009 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 42 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