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Crystal structure of RbcX from Anabaena CA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PEN PDB entry 2PEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 1.0 M Ammonium phosphate, 0.1 M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.021 α = 90 b = 69.021 β = 90 c = 113.805 γ = 120
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 MARMOSAIC 225 mm CCD 2006-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.07200 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 59.774 98.1 0.078 0.078 8.3 3.6 11805 41.512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 88.2 0.444 0.444 1.7 2.9 1542
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 2PEN 2.5 20 10630 502 99.84 0.244 0.241 0.2405 0.298 0.3005 RANDOM 41.152
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] 2.31 1.16 2.31 -3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.735 r_dihedral_angle_4_deg 28.005 r_dihedral_angle_3_deg 21.533 r_dihedral_angle_1_deg 6.571 r_scangle_it 3.432 r_scbond_it 2.067 r_angle_refined_deg 1.448 r_mcangle_it 1.259 r_mcbond_it 0.726 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.735 r_dihedral_angle_4_deg 28.005 r_dihedral_angle_3_deg 21.533 r_dihedral_angle_1_deg 6.571 r_scangle_it 3.432 r_scbond_it 2.067 r_angle_refined_deg 1.448 r_mcangle_it 1.259 r_mcbond_it 0.726 r_nbtor_refined 0.304 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.226 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1755 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction MOLREP phasing