4XMF

Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 complexed with histamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27725%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8, 0.25%(w/v) Gly-Gly, 0.25%(w/v) Gly-Gly-Gly, 0.25%(w/v) Gly- Gly-Gly-Gly, 0.25%(w/v) pentaglycine, 0.02 M HEPES sodium pH 6.8.
Crystal Properties
Matthews coefficientSolvent content
2.1342.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.338α = 90
b = 66.722β = 116.87
c = 38.825γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.630.7496.90.06715.33.822417
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)
11.61.6495.50.781.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTFREE R-VALUE3MVF1.630.741.9922417112197.260.16090.15830.2071
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]
1.7164-1.3211-0.462-1.2544
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.442
f_angle_d1.024
f_chiral_restr0.077
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1461
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms51

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing