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Rubisco from Skeletonema marinoi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.05 M HEPES pH 7.5, 0.05 M NaCl, 7-13% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.022 α = 90 b = 111.022 β = 90 c = 396.361 γ = 90
Symmetry Space Group P 41 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 100 CCD MAR CCD 165 mm 2004-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.087 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 2.6 19.96 96.9 0.178 4.2 9.3 75003
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 2.6 2.69 75.8 0.956
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 5MZ2 2.6 19.96 70943 3822 96.9 0.175 0.171 0.1763 0.238 0.2362 RANDOM 28.76
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.655 r_dihedral_angle_4_deg 16.063 r_dihedral_angle_3_deg 14.304 r_dihedral_angle_1_deg 7.482 r_long_range_B_refined 2.228 r_long_range_B_other 2.22 r_angle_refined_deg 1.556 r_mcangle_it 1.16 r_mcangle_other 1.16 r_angle_other_deg 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.655 r_dihedral_angle_4_deg 16.063 r_dihedral_angle_3_deg 14.304 r_dihedral_angle_1_deg 7.482 r_long_range_B_refined 2.228 r_long_range_B_other 2.22 r_angle_refined_deg 1.556 r_mcangle_it 1.16 r_mcangle_other 1.16 r_angle_other_deg 1.015 r_scangle_other 0.923 r_mcbond_it 0.65 r_mcbond_other 0.65 r_scbond_it 0.507 r_scbond_other 0.507 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19532 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing