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Crystal Structure of a RuBisCO-like Protein rlp2 from Rhodopseudomonas palustris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YKW PDB ENTRY 1YKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 280mM ammonium acetate, 100mM sodium acetate, 30% PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.662 α = 90 b = 119.529 β = 90 c = 203.04 γ = 90
Symmetry Space Group P 21 21 21
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 2004-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9537 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 3.3 90 99.7 0.164 9.6 6.2 26399 26399
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 3.3 3.42 99.5 0.467 3.8 5.6 2572
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 1YKW 3.3 77.38 24549 24549 1307 99.73 0.20402 0.20402 0.2025 0.202 0.23228 0.2267 RANDOM 35.223
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] -1 0.17 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.048 r_dihedral_angle_3_deg 21.041 r_dihedral_angle_4_deg 20.89 r_dihedral_angle_1_deg 5.944 r_scangle_it 2.385 r_angle_refined_deg 1.396 r_scbond_it 1.31 r_mcangle_it 1.102 r_mcbond_it 0.601 r_symmetry_vdw_refined 0.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.048 r_dihedral_angle_3_deg 21.041 r_dihedral_angle_4_deg 20.89 r_dihedral_angle_1_deg 5.944 r_scangle_it 2.385 r_angle_refined_deg 1.396 r_scbond_it 1.31 r_mcangle_it 1.102 r_mcbond_it 0.601 r_symmetry_vdw_refined 0.386 r_nbtor_refined 0.317 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13012 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing