1SQ7

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 DROP5.2295PEG 6000, citrate, t-butanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5852.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.67α = 90
b = 61.67β = 90
c = 500.886γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBent mirror2002-06-15MSINGLE 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)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
12.83094.30.08310.426.62162361531120.4
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)
12.762.9382.40.11775.292572

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 8TIM2.8528.2813977132796981000.204680.204680.202140.25185RANDOM3.209
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]
1.410.711.41-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.193
r_angle_refined_deg1.074
r_angle_other_deg0.837
r_scangle_it0.488
r_scbond_it0.293
r_nbd_other0.212
r_symmetry_vdw_other0.171
r_mcangle_it0.165
r_nbd_refined0.159
r_xyhbond_nbd_refined0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.193
r_angle_refined_deg1.074
r_angle_other_deg0.837
r_scangle_it0.488
r_scbond_it0.293
r_nbd_other0.212
r_symmetry_vdw_other0.171
r_mcangle_it0.165
r_nbd_refined0.159
r_xyhbond_nbd_refined0.133
r_symmetry_vdw_refined0.099
r_mcbond_it0.089
r_symmetry_hbond_refined0.082
r_nbtor_other0.078
r_chiral_restr0.05
r_bond_refined_d0.01
r_bond_other_d0.003
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3744
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
AMoREphasing