3HM6 | pdb_00003hm6

Crystal structure of the cytoplasmic domain of human plexin B1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherFor phasing, native crystals were incubated over-night in an artificial mother liquor containing 0.001 M thimerosal.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829116% peg-2000 mme, 0.1M TRIS, 0.2M TMAO, pH 8, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3948.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.346α = 90
b = 74.346β = 90
c = 214.398γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152007-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9999NSLSX25

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
12.43099.90.045159.827657
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)
12.42.4999.90.5777.62703

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTFor phasing, native crystals were incubated over-night in an artificial mother liquor containing 0.001 M thimerosal.2.40228.08327598139099.7790.2280.2270.290.2620.31RANDOM47.297
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]
0.9530.4760.953-1.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.655
r_dihedral_angle_4_deg17.721
r_dihedral_angle_3_deg14.896
r_dihedral_angle_1_deg5.576
r_mcangle_it2.886
r_scangle_it2.695
r_mcbond_it1.932
r_scbond_it1.923
r_angle_refined_deg1.213
r_angle_other_deg0.899
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4078
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms19

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling