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Crystal structure of CbbY (AT3G48420) from Arabidobsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UAR PDB entry 4UAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 25 % (wt/vol) PEG-6000 and 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.725 α = 90 b = 140.041 β = 90 c = 87.107 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2012-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.000 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.3 70.021 97.9 0.049 0.058 0.029 13.2 3.7 70347 70347
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 95.3 0.624 0.624 0.37 1.2 3.6 9877
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 4UAR 1.3 30 70149 3530 97.38 0.1381 0.1363 0.1354 0.172 0.1703 RANDOM 17.581
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] -0.56 -0.54 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_sphericity_free 30.412 r_dihedral_angle_4_deg 22.351 r_dihedral_angle_3_deg 13.157 r_sphericity_bonded 10.97 r_rigid_bond_restr 6.645 r_dihedral_angle_1_deg 5.544 r_angle_refined_deg 2.086 r_angle_other_deg 0.974 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_sphericity_free 30.412 r_dihedral_angle_4_deg 22.351 r_dihedral_angle_3_deg 13.157 r_sphericity_bonded 10.97 r_rigid_bond_restr 6.645 r_dihedral_angle_1_deg 5.544 r_angle_refined_deg 2.086 r_angle_other_deg 0.974 r_chiral_restr 0.145 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1866 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 1
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction REFMAC refinement XDS data reduction XSCALE data reduction