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Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroides in complex with Xylulose-(1,5)bisphosphate, crystal form I
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 6.5 291 25 % PEG-550MME, 0.1 M MES-NaOH pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.419 α = 90 b = 51.468 β = 94.06 c = 122.083 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 2M 2013-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.97639 SLS X06DA
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 1.3 121.776 99.5 0.066 0.074 0.033 13.2 4.7 107256 107256
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 97.4 0.839 0.839 0.451 0.9 4.2 15268
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 107186 5342 99.43 0.1235 0.1212 0.1206 0.1685 0.169 RANDOM 16.916
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] 1.07 -0.2 -0.26 -0.79
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.806 r_dihedral_angle_2_deg 30.413 r_dihedral_angle_4_deg 19.755 r_dihedral_angle_3_deg 13.018 r_sphericity_bonded 11.348 r_dihedral_angle_1_deg 6.244 r_rigid_bond_restr 6.034 r_angle_refined_deg 2.049 r_angle_other_deg 0.955 r_chiral_restr 0.249
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.806 r_dihedral_angle_2_deg 30.413 r_dihedral_angle_4_deg 19.755 r_dihedral_angle_3_deg 13.018 r_sphericity_bonded 11.348 r_dihedral_angle_1_deg 6.244 r_rigid_bond_restr 6.034 r_angle_refined_deg 2.049 r_angle_other_deg 0.955 r_chiral_restr 0.249 r_bond_refined_d 0.021 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 3466 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms 62
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction REFMAC refinement XSCALE data reduction