1SU5

Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8TIMPDB entry 8TIM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5294Citrate, ammonium sulphate, sodium chloride, 2-phosphoglycolate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.8957.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.756α = 90
b = 86.756β = 90
c = 163.376γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBent mirror2001-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.6100990.1090.09516.58.7201071990619.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.592.6997.50.3920.3825.21961

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 8TIM2.717.79176981679590399.70.187260.187260.184650.23638RANDOM15.207
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]
2.182.18-4.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.405
r_scangle_it1.459
r_angle_refined_deg1.235
r_scbond_it1.088
r_angle_other_deg0.778
r_mcangle_it0.488
r_symmetry_vdw_other0.297
r_mcbond_it0.268
r_nbd_other0.251
r_symmetry_hbond_refined0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.405
r_scangle_it1.459
r_angle_refined_deg1.235
r_scbond_it1.088
r_angle_other_deg0.778
r_mcangle_it0.488
r_symmetry_vdw_other0.297
r_mcbond_it0.268
r_nbd_other0.251
r_symmetry_hbond_refined0.246
r_xyhbond_nbd_refined0.213
r_nbd_refined0.206
r_symmetry_vdw_refined0.143
r_nbtor_other0.087
r_chiral_restr0.067
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3736
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing