3QC3

Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62770.16M magnesium acetate, 10.0% polyethylene glycol 8000, 20.0% Glycerol, 0.1M sodium cacodylate pH 6.0, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4850.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.665α = 90
b = 47.665β = 90
c = 220.774γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFLAT MIRROR (VERTICAL FOCUSING)2009-12-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97944,0.97894SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.229.12797.60.0958.3524823-330.791
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2896.40.6511.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.229.12724753126399.570.16670.16440.2112RANDOM46.987
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]
1.761.76-3.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.536
r_dihedral_angle_4_deg18.958
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg4.298
r_scangle_it2.849
r_scbond_it2.018
r_angle_refined_deg1.614
r_mcangle_it1.108
r_angle_other_deg1.029
r_mcbond_it0.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.536
r_dihedral_angle_4_deg18.958
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg4.298
r_scangle_it2.849
r_scbond_it2.018
r_angle_refined_deg1.614
r_mcangle_it1.108
r_angle_other_deg1.029
r_mcbond_it0.609
r_mcbond_other0.176
r_chiral_restr0.094
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3399
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms18

Software

Software
Software NamePurpose
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing