2XSX | pdb_00002xsx

Crystal structure of human beta enolase ENOB


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TE6PDB ENTRIES 1TE6, 2AKM, 2AKZ, 2PSN AND 3B97
experimental modelPDB 2AKMPDB ENTRIES 1TE6, 2AKM, 2AKZ, 2PSN AND 3B97
experimental modelPDB 2AKZPDB ENTRIES 1TE6, 2AKM, 2AKZ, 2PSN AND 3B97
experimental modelPDB 2PSNPDB ENTRIES 1TE6, 2AKM, 2AKZ, 2PSN AND 3B97
experimental modelPDB 3B97PDB ENTRIES 1TE6, 2AKM, 2AKZ, 2PSN AND 3B97

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M NA_ACETATE, 25% PEG_8000, 0.1M CACODYLATE PH 7
Crystal Properties
Matthews coefficientSolvent content
2.6553.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.878α = 90
b = 105.531β = 90
c = 106.091γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.729.4996.40.0915.78.7114102216.9
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)
11.71.7994.60.723.18.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1TE6, 2AKM, 2AKZ, 2PSN AND 3B971.729.39108327569796.080.154630.152820.160.189050.2RANDOM19.721
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]
-0.491.24-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.331
r_dihedral_angle_4_deg15.647
r_dihedral_angle_3_deg12.89
r_dihedral_angle_1_deg5.99
r_scangle_it5.422
r_scbond_it4.339
r_mcangle_it3.094
r_mcbond_it2.544
r_angle_other_deg2.069
r_angle_refined_deg1.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.331
r_dihedral_angle_4_deg15.647
r_dihedral_angle_3_deg12.89
r_dihedral_angle_1_deg5.99
r_scangle_it5.422
r_scbond_it4.339
r_mcangle_it3.094
r_mcbond_it2.544
r_angle_other_deg2.069
r_angle_refined_deg1.525
r_mcbond_other1.103
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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_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 Atoms6592
Nucleic Acid Atoms
Solvent Atoms1083
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing