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Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GK8 PDB ENTRY 1GK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.44 49.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.242 α = 90 b = 169.14 β = 96.24 c = 137.179 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 MARRESEARCH 2004-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 20 98.4 0.09 11.9 7.9 125065
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 98.6 0.63
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 ENTRY 1GK8 2.8 20 118598 6228 98.4 0.198 0.197 0.228 0.1784 RANDOM 59.6
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] 5.18 -2.01 -2.54 -3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.096 r_dihedral_angle_3_deg 16.682 r_dihedral_angle_4_deg 15.392 r_dihedral_angle_1_deg 6.305 r_scangle_it 2.044 r_angle_refined_deg 1.356 r_scbond_it 1.24 r_mcangle_it 1.08 r_mcbond_it 0.612 r_symmetry_vdw_refined 0.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.096 r_dihedral_angle_3_deg 16.682 r_dihedral_angle_4_deg 15.392 r_dihedral_angle_1_deg 6.305 r_scangle_it 2.044 r_angle_refined_deg 1.356 r_scbond_it 1.24 r_mcangle_it 1.08 r_mcbond_it 0.612 r_symmetry_vdw_refined 0.422 r_symmetry_hbond_refined 0.335 r_nbtor_refined 0.314 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37837 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 272
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing