5Z6U

Crystal structure of D-xylose reductase from Scheffersomyces stipitis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 3350, Ammonium citrate tribasic
Crystal Properties
Matthews coefficientSolvent content
2.5752.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.248α = 90
b = 87.151β = 90
c = 122.623γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702017-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.9571.0498.80.20855.26.751177
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.980.208

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 REPLACEMENTTHROUGHOUT1Z9A1.9571.0451177272598.430.19140.1890.2358RANDOM36.514
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]
-2.68-13.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.621
r_dihedral_angle_4_deg19.69
r_dihedral_angle_3_deg13.399
r_dihedral_angle_1_deg6.021
r_angle_refined_deg1.76
r_angle_other_deg1.042
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.621
r_dihedral_angle_4_deg19.69
r_dihedral_angle_3_deg13.399
r_dihedral_angle_1_deg6.021
r_angle_refined_deg1.76
r_angle_other_deg1.042
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5084
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms12

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing