3RLH

Crystal structure of a class II phospholipase D from Loxosceles intermedia venom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XX1PDB ENTRY 1XX1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52910.1 M Tris-HCl pH 7.5, 40%(v/v) PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.8132.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.81α = 90
b = 49.3β = 105.83
c = 56.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.458LNLSW01B-MX2

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
11.7254.16599.928077280416
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.8199.90.4680.46823.54040

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1XX11.7254.162943428026140899.830.1740.1740.17180.2143RANDOM17.8137
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]
1.620.630.63-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.842
r_dihedral_angle_4_deg20.591
r_dihedral_angle_3_deg13.25
r_dihedral_angle_1_deg6.176
r_scangle_it4.816
r_scbond_it3.206
r_mcangle_it1.97
r_angle_refined_deg1.93
r_mcbond_it1.215
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.842
r_dihedral_angle_4_deg20.591
r_dihedral_angle_3_deg13.25
r_dihedral_angle_1_deg6.176
r_scangle_it4.816
r_scbond_it3.206
r_mcangle_it1.97
r_angle_refined_deg1.93
r_mcbond_it1.215
r_chiral_restr0.149
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2188
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms47

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
SCALAdata scaling