3I5W

Crystal structure of human alpha-defensin 5 (mutant R13H)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.627320% PEG 4000, 20% 2-propanol, 0.1M Na citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.652.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.018α = 90
b = 49.754β = 90
c = 62.355γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVconfocal2009-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
11.6338.89197.70.07526.76.896539433
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)
11.631.6681.60.5123.46.2399

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1ZMP1.63202942945697.820.1770.1760.194RANDOM28.288
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]
-0.02-0.790.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.497
r_dihedral_angle_4_deg11.917
r_dihedral_angle_3_deg11.534
r_dihedral_angle_1_deg6.546
r_scangle_it5.272
r_scbond_it3.038
r_mcangle_it2.021
r_angle_refined_deg1.733
r_mcbond_it1.208
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.497
r_dihedral_angle_4_deg11.917
r_dihedral_angle_3_deg11.534
r_dihedral_angle_1_deg6.546
r_scangle_it5.272
r_scbond_it3.038
r_mcangle_it2.021
r_angle_refined_deg1.733
r_mcbond_it1.208
r_chiral_restr0.119
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms488
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing