6ZR3

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with N-acetyl-galactosamine-4-sulfate ligand bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4M7Hpdbid 4M7H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.7 M Ammonium Sulphate, 8% Dioxane, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.0559.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.019α = 90
b = 119.019β = 90
c = 44.31γ = 90
Symmetry
Space GroupP 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.9753.2897.30.1020.1180.0560.9767.53.942961
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.0298.10.270.3220.1720.8883.1

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 REPLACEMENTTHROUGHOUTpdbid 4M7H1.9753.2840849207096.510.18620.18430.2258RANDOM23.457
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]
0.80.8-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.807
r_dihedral_angle_4_deg18.183
r_dihedral_angle_3_deg13.04
r_dihedral_angle_1_deg7.544
r_angle_refined_deg1.351
r_angle_other_deg1.281
r_chiral_restr0.063
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.807
r_dihedral_angle_4_deg18.183
r_dihedral_angle_3_deg13.04
r_dihedral_angle_1_deg7.544
r_angle_refined_deg1.351
r_angle_other_deg1.281
r_chiral_restr0.063
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3514
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms70

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing