4UAU

Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroides in complex with Xylulose-(1,5)bisphosphate, crystal form II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UARPDB entry 4UAR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529125 % PEG-1000, 0.1 M MES-NaOH pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2445.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.288α = 90
b = 69.767β = 90
c = 125.793γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.97639SLSX06DA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4546.71599.20.0650.0710.028176.38024480244
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)RedundancyNumber Unique Reflections (All)
11.451.5394.80.710.710.3531.14.711061

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4UAR1.453080090407599.140.18020.17850.2108RANDOM23.354
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]
0.030.63-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.175
r_dihedral_angle_4_deg16.678
r_dihedral_angle_3_deg12.54
r_dihedral_angle_1_deg5.861
r_scangle_it3.672
r_scbond_it2.229
r_mcangle_it1.417
r_angle_refined_deg1.403
r_mcbond_it0.784
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.175
r_dihedral_angle_4_deg16.678
r_dihedral_angle_3_deg12.54
r_dihedral_angle_1_deg5.861
r_scangle_it3.672
r_scbond_it2.229
r_mcangle_it1.417
r_angle_refined_deg1.403
r_mcbond_it0.784
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3475
Nucleic Acid Atoms
Solvent Atoms590
Heterogen Atoms62

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
HKLdata reduction