1ZOR

Isocitrate dehydrogenase from the hyperthermophile Thermotoga maritima


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LWD1LWD, 1T0L
experimental modelPDB 1T0L1LWD, 1T0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6291PEG 6000, Sodium Acetate, Succinate, NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.754.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.47α = 90
b = 88.051β = 90
c = 180.926γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7110.996MAX III711

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
12.2435.5699.70.06615.844.849143489901.3840.94
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)
12.242.291000.3793.322500

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1LWD, 1T0L2.2435.561.384898846511247799.740.186470.186470.184490.22317RANDOM45.332
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]
2.41-3.050.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.321
r_dihedral_angle_4_deg21.497
r_dihedral_angle_3_deg16.376
r_dihedral_angle_1_deg6.496
r_scangle_it2.658
r_scbond_it1.646
r_angle_refined_deg1.251
r_mcangle_it0.87
r_mcbond_it0.454
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.321
r_dihedral_angle_4_deg21.497
r_dihedral_angle_3_deg16.376
r_dihedral_angle_1_deg6.496
r_scangle_it2.658
r_scbond_it1.646
r_angle_refined_deg1.251
r_mcangle_it0.87
r_mcbond_it0.454
r_nbtor_refined0.303
r_nbd_refined0.203
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.155
r_metal_ion_refined0.153
r_symmetry_hbond_refined0.142
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6358
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing