4UUI

A case study for twinned data analysis: multiple crystal forms of the enzyme N-acetyl-neuraminic lyase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XFWPDB ENTRY 2XFW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.2100MM TRIS-HCL PH 8.2, 200MM NACL, 18% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5852.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.985α = 90
b = 116.665β = 118.06
c = 83.678γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.873.921000.1217.21220532
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)
11.81.91000.534.97.3

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 2XFW1.7973.85115868614798.440.156830.155390.18383RANDOM12.828
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]
5.61-0.767.27-12.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.321
r_dihedral_angle_4_deg19.319
r_dihedral_angle_3_deg11.917
r_dihedral_angle_1_deg5.494
r_angle_refined_deg1.134
r_angle_other_deg0.854
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.321
r_dihedral_angle_4_deg19.319
r_dihedral_angle_3_deg11.917
r_dihedral_angle_1_deg5.494
r_angle_refined_deg1.134
r_angle_other_deg0.854
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms9270
Nucleic Acid Atoms
Solvent Atoms745
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement