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Crystal Structure Analysis of Ard1 from Thermoplasma volcanium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 Tris, HCl, potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.48 64.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.24 α = 90 b = 129.935 β = 93.94 c = 158.576 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 270 Mirror 2012-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0000 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.3 50 60855 57796
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.36
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 MOLECULAR REPLACEMENT THROUGHOUT 2X7B 3.32 49.59 60855 57758 3078 99.13 0.20729 0.20522 0.2059 0.2462 0.2448 RANDOM 86.965
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] -5.51 1.41 2.92 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_dihedral_angle_4_deg 16.969 r_dihedral_angle_3_deg 16.942 r_mcangle_it 9.123 r_dihedral_angle_1_deg 7.233 r_scbond_it 6.058 r_mcbond_it 5.848 r_mcbond_other 5.847 r_angle_refined_deg 1.575 r_angle_other_deg 0.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_dihedral_angle_4_deg 16.969 r_dihedral_angle_3_deg 16.942 r_mcangle_it 9.123 r_dihedral_angle_1_deg 7.233 r_scbond_it 6.058 r_mcbond_it 5.848 r_mcbond_other 5.847 r_angle_refined_deg 1.575 r_angle_other_deg 0.833 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19559 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 405
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing