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Crystal Structure of a Novel RuBisCO-Like Protein from the Green Sulfur Bacterium Chlorobium tepidum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5RUB PDB ENTRY 5RUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 PEG 3350, magnesium formate , pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.348 α = 90 b = 78.451 β = 99.95 c = 90.369 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2003-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.1271 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 90 97.5 0.129 7.7 3.1 60951 60951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 84.7 0.397 2 2 5253
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5RUB 2 87.71 57608 57608 2956 97.91 0.20329 0.20329 0.20114 0.2012 0.24539 0.2451 RANDOM 28.441
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] -2.18 0.67 -0.74 3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.166 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 17.018 r_dihedral_angle_1_deg 6.703 r_scangle_it 3.82 r_scbond_it 2.46 r_angle_refined_deg 1.626 r_mcangle_it 1.598 r_mcbond_it 1.018 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.166 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 17.018 r_dihedral_angle_1_deg 6.703 r_scangle_it 3.82 r_scbond_it 2.46 r_angle_refined_deg 1.626 r_mcangle_it 1.598 r_mcbond_it 1.018 r_nbtor_refined 0.305 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.166 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.117 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 6398 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing