X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GDH1GDH, 1WWK as a basis of 2-member ensemble
experimental modelPDB 1WWK1GDH, 1WWK as a basis of 2-member ensemble

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (12% PEG 3350, 0.10 M MOPS PH 7). Crystal was cryo-protected with 15% PEG 3350, 0.10 M PIPES PH 6.5 and a final concentration of 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5852.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.996α = 90
b = 66.436β = 98.59
c = 148.774γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2006-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97928APS23-ID-D

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
12.4549.32693.30.1577.0876.250144
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)
12.452.5180.30.5042.2614.82832

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GDH, 1WWK as a basis of 2-member ensemble2.4549.32650129255193.1140.210.20720.2643RANDOM8.853
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]
-0.69-1.165-0.4270.769
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.26
r_dihedral_angle_4_deg22.585
r_dihedral_angle_3_deg17.416
r_dihedral_angle_1_deg6.344
r_scangle_it5.649
r_scbond_it3.723
r_mcangle_it1.682
r_angle_refined_deg1.59
r_mcbond_it0.951
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.26
r_dihedral_angle_4_deg22.585
r_dihedral_angle_3_deg17.416
r_dihedral_angle_1_deg6.344
r_scangle_it5.649
r_scbond_it3.723
r_mcangle_it1.682
r_angle_refined_deg1.59
r_mcbond_it0.951
r_nbtor_refined0.309
r_symmetry_hbond_refined0.255
r_symmetry_vdw_refined0.248
r_nbd_refined0.219
r_xyhbond_nbd_refined0.179
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9768
Nucleic Acid Atoms
Solvent Atoms450
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction