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Crystal structure of Pyrococcus horikoshii a plant- and prokaryote-conserved (PPC) protein at 1.60 resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 1.8M ammonium sulphate, 0.2M potassium sodium tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.922 α = 90 b = 53.922 β = 90 c = 159.181 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 100 CCD ADSC QUANTUM 210 2004-04-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9794, 0.9796, 0.9744, 0.9843 SPring-8 BL41XU
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 1.6 18.83 95.67 17768 17768 15.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.6 10 17247 17247 925 95.67 0.16531 0.16531 0.16379 0.2022 0.1932 0.2053 RANDOM 11.736
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_1_deg 7.31 r_angle_refined_deg 1.519 r_angle_other_deg 0.792 r_symmetry_vdw_other 0.315 r_nbd_other 0.255 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.14 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.31 r_angle_refined_deg 1.519 r_angle_other_deg 0.792 r_symmetry_vdw_other 0.315 r_nbd_other 0.255 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.14 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.109 r_nbtor_other 0.085 r_bond_refined_d 0.022 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1137 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement SOLVE phasing