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Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation
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 2.01 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.377 α = 90 b = 177.446 β = 117.65 c = 122.568 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 200 CCD ADSC CCD 2003-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.8 30 92.4 0.23 16.5 14.8 389935
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 1.8 1.83 60 0.46 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 PDB ENTRY 1GK8 1.8 30 369935 19621 92.1 0.193 0.191 0.1928 0.214 0.1948 RANDOM 15.05
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] 0.44 -0.05 -0.02 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.604 r_dihedral_angle_4_deg 15.644 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 5.631 r_scangle_it 2.795 r_scbond_it 1.73 r_angle_refined_deg 1.108 r_mcangle_it 1.043 r_mcbond_it 0.654 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.604 r_dihedral_angle_4_deg 15.644 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 5.631 r_scangle_it 2.795 r_scbond_it 1.73 r_angle_refined_deg 1.108 r_mcangle_it 1.043 r_mcbond_it 0.654 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.133 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.08 r_metal_ion_refined 0.024 r_bond_refined_d 0.008 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_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 38134 Nucleic Acid Atoms Solvent Atoms 2892 Heterogen Atoms 360
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing