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Crystal structure of octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Pyrococcus horikoshii OT3 (form-1 crystal)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 NaCl, PEG6000, Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.992 α = 90 b = 143.992 β = 90 c = 101.417 γ = 90
Symmetry Space Group P 4 21 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 IMAGE PLATE RIGAKU RAXIS V 2005-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00000 SPring-8 BL26B1
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 2 50 71958 22.6
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 THROUGHOUT 2 50 68293 3636 99.75 0.17797 0.17624 0.1826 0.21018 0.1756 RANDOM 28.35
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.544 r_scangle_it 4.679 r_scbond_it 2.763 r_mcangle_it 1.789 r_angle_refined_deg 1.494 r_mcbond_it 0.919 r_angle_other_deg 0.863 r_symmetry_vdw_other 0.334 r_symmetry_vdw_refined 0.304 r_nbd_other 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.544 r_scangle_it 4.679 r_scbond_it 2.763 r_mcangle_it 1.789 r_angle_refined_deg 1.494 r_mcbond_it 0.919 r_angle_other_deg 0.863 r_symmetry_vdw_other 0.334 r_symmetry_vdw_refined 0.304 r_nbd_other 0.238 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.107 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6493 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing