2BOX

EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with strontium.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BOUPDB ENTRY 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M STRONTIUM CHLORIDE, 12-16% W/V PEG 8000, 0.1 M NA CACODYLATE BUFFER PH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.261.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.106α = 90
b = 61.575β = 90
c = 35.495γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2002-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.423.2699.50.114.84.482700.083
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)
12.42.5397.60.112.13.8

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 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN)2.523.262734273423730.24260.24260.24030.2844RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
t_dihedral_angle_d17.765
t_it0.778
t_angle_deg0.641
t_nbd0.035
t_gen_planes0.012
t_trig_c_planes0.005
t_bond_d0.003
t_incorr_chiral_ct
t_pseud_angle
t_omega_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_dihedral_angle_d17.765
t_it0.778
t_angle_deg0.641
t_nbd0.035
t_gen_planes0.012
t_trig_c_planes0.005
t_bond_d0.003
t_incorr_chiral_ct
t_pseud_angle
t_omega_torsion
t_other_torsion
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1014
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms8

Software

Software
Software NamePurpose
TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing