5DAY

The structure of NAP1-Related Protein(NRP1) in Arabidopsis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.6289.1525% PEG 400, 0.1 M HEPES pH 7.6, 0.2 M Calcium chloride dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.5952.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.542α = 90
b = 60.812β = 90
c = 135.248γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97900, 0.97946, 0.97930, 0.95365SSRFBL17U

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
12.3295099.50.05543.7621817
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.332.411969

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADFREE R-VALUE2.32945.2181.4421784200498.830.23360.230.2688
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.468
f_angle_d0.833
f_chiral_restr0.048
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2841
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms3

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Cootdata scaling
PHENIXphasing