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Crystal structure of the complex of sulfate ion and octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Pyrococcus horikoshii OT3 (form-2 crystal)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CWX PDB ID: 2CWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 Ammonium sulfate, sodium bicarbonate, magnesium chloride, sodium acetate, 2cabp, Tris-HCl , pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.591 α = 90 b = 148.774 β = 126.49 c = 108.452 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS V 2005-09-30 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 1.9 50 162742
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID: 2CWX 1.9 50 154541 8084 94.26 0.18121 0.17973 0.20922 0.2112 RANDOM 19.426
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] 0.91 1.67 -1.49 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.692 r_scangle_it 4.066 r_scbond_it 2.578 r_angle_refined_deg 1.662 r_mcangle_it 1.604 r_mcbond_it 0.91 r_angle_other_deg 0.896 r_symmetry_vdw_other 0.293 r_nbd_other 0.243 r_nbd_refined 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.692 r_scangle_it 4.066 r_scbond_it 2.578 r_angle_refined_deg 1.662 r_mcangle_it 1.604 r_mcbond_it 0.91 r_angle_other_deg 0.896 r_symmetry_vdw_other 0.293 r_nbd_other 0.243 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.109 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 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 13217 Nucleic Acid Atoms Solvent Atoms 750 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing