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Crystal structure of Type III Rubisco complexed with 2-CABP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GEH PDB ENTRY 1GEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M Acetate, 0.1M CaCl2, 5% PEG6000, 10% MPD, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.287 α = 90 b = 246.377 β = 90 c = 144.589 γ = 90
Symmetry Space Group P 21 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 95 CCD ADSC QUANTUM 210 2008-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 2.3 50 99.9 0.105 15.2 271962 26.4
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) 2.3 2.34 100 0.379 3.9
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 PDB ENTRY 1GEH 2.3 35.39 257731 13630 99.55 0.20116 0.19887 0.1999 0.24429 0.2424 RANDOM 25.083
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] 4.52 -2.27 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.821 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 14.192 r_dihedral_angle_1_deg 5.23 r_scangle_it 2.142 r_scbond_it 1.274 r_angle_refined_deg 0.995 r_mcangle_it 0.822 r_mcbond_it 0.421 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.821 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 14.192 r_dihedral_angle_1_deg 5.23 r_scangle_it 2.142 r_scbond_it 1.274 r_angle_refined_deg 0.995 r_mcangle_it 0.822 r_mcbond_it 0.421 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 34125 Nucleic Acid Atoms Solvent Atoms 2306 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing