1SSD

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, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.9758.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.422α = 90
b = 88.422β = 90
c = 161.874γ = 90
Symmetry
Space GroupP 41 21 2

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
12.919.7398.80.1050.09515.15.41204632021731.1
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)
12.999.40.2980.3557.12007

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 8TIM2.919.7147601399676499.240.157940.157940.156110.19287RANDOM25.34
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.04
r_scangle_it1.684
r_angle_refined_deg1.188
r_scbond_it0.938
r_angle_other_deg0.76
r_mcangle_it0.537
r_mcbond_it0.261
r_nbd_other0.229
r_symmetry_vdw_other0.228
r_xyhbond_nbd_refined0.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.04
r_scangle_it1.684
r_angle_refined_deg1.188
r_scbond_it0.938
r_angle_other_deg0.76
r_mcangle_it0.537
r_mcbond_it0.261
r_nbd_other0.229
r_symmetry_vdw_other0.228
r_xyhbond_nbd_refined0.218
r_nbd_refined0.19
r_symmetry_vdw_refined0.109
r_symmetry_hbond_refined0.097
r_nbtor_other0.084
r_chiral_restr0.06
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3742
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing