1SPQ

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 DROP9.1277PEG 6000, Tris, 2-phosphoglycolate, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3146.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.706α = 90
b = 57.334β = 92.89
c = 106.154γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBent mirror2003-02-10MSINGLE 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
12.134097.80.0570.062223.48258642526823.9
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)
12.132.2178.80.1450.1447.42035

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 8TIM2.1638.352526823998127096.050.162150.162150.160230.19779RANDOM11.296
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]
-1.190.92-1.292.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.931
r_mcangle_it1.588
r_scangle_it1.507
r_angle_refined_deg1.225
r_mcbond_it0.983
r_scbond_it0.962
r_angle_other_deg0.858
r_symmetry_vdw_other0.276
r_nbd_other0.221
r_symmetry_hbond_refined0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.931
r_mcangle_it1.588
r_scangle_it1.507
r_angle_refined_deg1.225
r_mcbond_it0.983
r_scbond_it0.962
r_angle_other_deg0.858
r_symmetry_vdw_other0.276
r_nbd_other0.221
r_symmetry_hbond_refined0.22
r_nbd_refined0.181
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.12
r_nbtor_other0.079
r_chiral_restr0.069
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3664
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing