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Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RBL PDB entry 1RBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.7 277 15-17 % 2-methyl-2,4-pentanediol, 0.1 M KCl, 0.1 M Tris-HCl, pH 8.7, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.24 71.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 244.75 α = 90 b = 244.75 β = 90 c = 99.669 γ = 90
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 315r 2009-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97908 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.2 47.999 84.8 0.109 0.109 8.9 3.2 41265 41265
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 48.7 0.311 0.311 2.4 2.3 3393
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 PDB entry 1RBL 3.2 30 43281 41214 2067 84.5 0.2175 0.216 0.2173 0.2454 0.2466 RANDOM 89.9627
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] 3.33 3.33 -6.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.153 r_dihedral_angle_3_deg 20.117 r_dihedral_angle_4_deg 17.329 r_dihedral_angle_1_deg 5.178 r_angle_refined_deg 1.073 r_scangle_it 0.954 r_scbond_it 0.546 r_mcangle_it 0.331 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.153 r_dihedral_angle_3_deg 20.117 r_dihedral_angle_4_deg 17.329 r_dihedral_angle_1_deg 5.178 r_angle_refined_deg 1.073 r_scangle_it 0.954 r_scbond_it 0.546 r_mcangle_it 0.331 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.183 r_mcbond_it 0.174 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10078 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XSCALE data scaling