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Crystal structure of Pndk from Bacillus anthracis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8
Crystal Properties Matthews coefficient Solvent content 2.1 36.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.531 α = 90 b = 107.531 β = 90 c = 52.301 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH YALE MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 26.7 99.9 0.09 14.9 6.3 12490 2
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 OTHER THROUGHOUT NONE 2 93.25 11540 931 99.63 0.17707 0.17348 0.175 0.22272 0.2208 RANDOM 26.369
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] -0.08 -0.04 -0.08 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.172 r_dihedral_angle_4_deg 29.035 r_dihedral_angle_3_deg 16.169 r_dihedral_angle_1_deg 5.84 r_scangle_it 5.39 r_scbond_it 3.091 r_mcangle_it 1.86 r_angle_refined_deg 1.5 r_mcbond_it 1.135 r_symmetry_hbond_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.172 r_dihedral_angle_4_deg 29.035 r_dihedral_angle_3_deg 16.169 r_dihedral_angle_1_deg 5.84 r_scangle_it 5.39 r_scbond_it 3.091 r_mcangle_it 1.86 r_angle_refined_deg 1.5 r_mcbond_it 1.135 r_symmetry_hbond_refined 0.333 r_nbtor_refined 0.309 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_refined 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_mcangle_other r_scbond_other 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 1170 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling