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Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroides in complex with Xylulose-(1,5)bisphosphate, crystal form II
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-1000, 0.1 M MES-NaOH pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.288 α = 90 b = 69.767 β = 90 c = 125.793 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 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 1.45 46.715 99.2 0.065 0.071 0.028 17 6.3 80244 80244
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 1.45 1.53 94.8 0.71 0.71 0.353 1.1 4.7 11061
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 1.45 30 80090 4075 99.14 0.1802 0.1785 0.1837 0.2108 0.2153 RANDOM 23.354
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] 0.03 0.63 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.175 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 5.861 r_scangle_it 3.672 r_scbond_it 2.229 r_mcangle_it 1.417 r_angle_refined_deg 1.403 r_mcbond_it 0.784 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.175 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 5.861 r_scangle_it 3.672 r_scbond_it 2.229 r_mcangle_it 1.417 r_angle_refined_deg 1.403 r_mcbond_it 0.784 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3475 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 62
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction REFMAC refinement XDS data reduction HKL data reduction