3UCC

Asymmetric complex of human neuron specific enolase-1-PGA/PEP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AKMPDB ENTRY 2AKM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529820% PEG4K, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4349.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.785α = 90
b = 119.677β = 90
c = 68.001γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-04-15SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
11.55087.50.08416.15.2131445
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)
11.51.5541.70.3471.66200

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2AKM1.536.44124405621182.890.22160.21970.2577RANDOM7.5783
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]
0.44-0.23-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.398
r_dihedral_angle_4_deg24.795
r_dihedral_angle_3_deg15.335
r_dihedral_angle_1_deg6.039
r_scangle_it5.947
r_scbond_it3.896
r_mcangle_it2.278
r_rigid_bond_restr2.224
r_angle_refined_deg1.939
r_mcbond_it1.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.398
r_dihedral_angle_4_deg24.795
r_dihedral_angle_3_deg15.335
r_dihedral_angle_1_deg6.039
r_scangle_it5.947
r_scbond_it3.896
r_mcangle_it2.278
r_rigid_bond_restr2.224
r_angle_refined_deg1.939
r_mcbond_it1.426
r_chiral_restr0.134
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6620
Nucleic Acid Atoms
Solvent Atoms601
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
CNSphasing