5A3L

Structure of Cea1A in complex with N-Acetylglucosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ASLPRUNED VERSION OF EPA1A-BASED PDB 4ASL MODELLER 9V7 MODEL OF PICA1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1277100 MM MAGNESIUMCHLORIDE, 100 MM SODIUM CHLORIDE, 100 MM SODIUMCITRATE PH 3.5, 12% PEG 4000, 5 MM N-ACETYLGLUCOSAMINE, 5 MM CALCIUMCHLORIDE, 277 K
Crystal Properties
Matthews coefficientSolvent content
2.7455.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.34α = 90
b = 106.21β = 90
c = 107.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MX-2552012-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.6619.8499.90.1145.8137801-3
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)
11.661.751000.593.35.8

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 REPLACEMENTTHROUGHOUTPRUNED VERSION OF EPA1A-BASED PDB 4ASL MODELLER 9V7 MODEL OF PICA11.6619.84135716208499.460.171190.170730.20206RANDOM16.277
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]
0.09-0.40.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.043
r_dihedral_angle_4_deg14.464
r_dihedral_angle_3_deg12.845
r_dihedral_angle_1_deg6.755
r_mcangle_it2.183
r_angle_refined_deg1.57
r_scbond_it1.479
r_angle_other_deg1.438
r_mcbond_it1.26
r_mcbond_other1.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.043
r_dihedral_angle_4_deg14.464
r_dihedral_angle_3_deg12.845
r_dihedral_angle_1_deg6.755
r_mcangle_it2.183
r_angle_refined_deg1.57
r_scbond_it1.479
r_angle_other_deg1.438
r_mcbond_it1.26
r_mcbond_other1.259
r_chiral_restr0.141
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.009
r_bond_other_d0.008
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6485
Nucleic Acid Atoms
Solvent Atoms1092
Heterogen Atoms181

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing