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Structure function studies of R. palustris RubisCO (S59F/M331A mutant; CABP-bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% Glycerol, 10 mM MgCl2, 20 mM NaHCO3. Reservoir solution: 20-24% PEG 3350, 200 mM sodium sulfate, 100 mM Bis-Tris Propane pH 7.0-8.0.
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.14 α = 90.03 b = 111.03 β = 101.69 c = 167.26 γ = 105.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9790 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 91.97 90.8 0.093 0.116 6 2.6 318354 -3 35.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 82.8 0.799 1.015 1.14 2.4
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 MOLECULAR REPLACEMENT THROUGHOUT 4LF1 2 20 317951 31796 91.07 0.2162 0.2126 0.2156 0.249 0.2529 RANDOM 42.42
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] -2.6687 -1.6104 -2.6151 -3.173 -2.1178 5.8417
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.91 t_other_torsion 2.67 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.91 t_other_torsion 2.67 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 82362 Nucleic Acid Atoms Solvent Atoms 2604 Heterogen Atoms 3120
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction