6ZQR

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with GlcNAc 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 DROP6.52931.5 M Ammonium Sulphate, 7% Dioxane, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.7755.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.6α = 90
b = 113.6β = 90
c = 44.08γ = 90
Symmetry
Space GroupP 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.9356.8698.70.0730.0860.0440.99712.43.542095
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)
11.931.9898.50.3790.4530.2430.7963.2

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 4M7H1.9356.840018207798.380.16830.16710.1912RANDOM18.312
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]
0.610.61-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.237
r_dihedral_angle_4_deg16.816
r_dihedral_angle_3_deg12.959
r_dihedral_angle_1_deg7.373
r_angle_refined_deg1.409
r_angle_other_deg1.346
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.237
r_dihedral_angle_4_deg16.816
r_dihedral_angle_3_deg12.959
r_dihedral_angle_1_deg7.373
r_angle_refined_deg1.409
r_angle_other_deg1.346
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3520
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms97

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction