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The structure of Halothiobacillus neapolitanus RuBisCo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RBL pdb entry 1rbl
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 298 ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.066 α = 90 b = 157.066 β = 90 c = 107.609 γ = 90
Symmetry Space Group I 4 2 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 ADSC QUANTUM 315 Double Crystal Si(111) 2003-11-13 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 1.8 90 0.091 19.4 9.4 62138 62138
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 1.8 1.86 100 0.355 8.7 10.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT pdb entry 1rbl 1.8 87.71 58984 58984 3095 99.95 0.14608 0.14502 0.1594 0.16574 0.1761 RANDOM 11.186
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] 0.49 0.49 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.893 r_scangle_it 4.207 r_scbond_it 2.665 r_mcangle_it 1.759 r_angle_refined_deg 1.519 r_mcbond_it 0.945 r_angle_other_deg 0.91 r_symmetry_hbond_refined 0.307 r_symmetry_vdw_other 0.304 r_nbd_other 0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.893 r_scangle_it 4.207 r_scbond_it 2.665 r_mcangle_it 1.759 r_angle_refined_deg 1.519 r_mcbond_it 0.945 r_angle_other_deg 0.91 r_symmetry_hbond_refined 0.307 r_symmetry_vdw_other 0.304 r_nbd_other 0.246 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.099 r_nbtor_other 0.085 r_gen_planes_other 0.022 r_bond_refined_d 0.015 r_gen_planes_refined 0.015 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 4369 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing