3FRP

Crystal Structure of Cobra Venom Factor, a Co-factor for C3- and C5 convertase CVFBb


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A74PDB ENTRY 2A74

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829313% PEG 3350, 10 mM MES pH 6.8, 5 mM CaCl2, 200 mM NH4Cl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7555.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.138α = 90
b = 151.141β = 90
c = 76.787γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCD2008-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
12.65091.90.0821.77.143934
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)
2.62.6973.90.3122.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2A742.615041713222191.160.250530.247990.29708RANDOM57.463
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]
1.84-0.41-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.228
r_dihedral_angle_3_deg18.299
r_dihedral_angle_4_deg17.327
r_dihedral_angle_1_deg6.251
r_scangle_it2.237
r_angle_refined_deg1.323
r_scbond_it1.318
r_mcangle_it1.016
r_mcbond_it0.536
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.228
r_dihedral_angle_3_deg18.299
r_dihedral_angle_4_deg17.327
r_dihedral_angle_1_deg6.251
r_scangle_it2.237
r_angle_refined_deg1.323
r_scbond_it1.318
r_mcangle_it1.016
r_mcbond_it0.536
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9076
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms1

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling