3OVR

Crystal Structure of hRPE and D-Xylulose 5-Phosphate Complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OVP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5289.150.2M Sodium Choloride, 0.1M BIS-TRIS, 25%(w/v) Polyethylene glycol 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K
Crystal Properties
Matthews coefficientSolvent content
1.9637.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.006α = 90
b = 43.665β = 94.69
c = 72.655γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS2010-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.765098.6382463824611.7

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3OVP1.94825.2230.1127840141197.130.14650.14410.191823.2694
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]
-1.80450.74462.1237-0.3191
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.605
f_angle_d1.017
f_chiral_restr0.07
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3350
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms104

Software

Software
Software NamePurpose
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling