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Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OEJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 24%peg 3350, 0.1 M tris-HCl, 0.2 M ammonium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.765 α = 90 b = 59.545 β = 103.24 c = 109.282 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 4 mirrors 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
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 25 98.3 0.044 74695 74695 11.9
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 (All) 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 20EJ 1.8 24.83 74695 74695 3762 98.3 0.188 0.185 0.185 0.1845 0.208 0.2072 RANDOM 16.5
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] -0.62 -1.86 6.28 -5.66
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 2.65 c_scbond_it 1.85 c_mcangle_it 1.48 c_angle_deg 1.3 c_mcbond_it 1.02 c_improper_angle_d 0.86 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6338 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing