X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.527710mM o-phosphorylethamine+ 2mM GTP crystallized in 0.1M Sodium Acetate trihydrate pH 4.5 and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.50
Crystal Properties
Matthews coefficientSolvent content
2.0540.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.971α = 90
b = 57.211β = 109.69
c = 80.886γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-2MIRRORS2003-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.232.2599.20.1233.13.725715
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)
2.212.2994.10.2761.82.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BD92.232.242440022343241996.350.189570.181920.26104RANDOM14.515
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]
-0.670.450.130.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.11
r_dihedral_angle_3_deg13.471
r_dihedral_angle_4_deg13.3
r_mcangle_it8.464
r_mcbond_it5.765
r_dihedral_angle_1_deg4.296
r_scangle_it3.918
r_scbond_it2.44
r_angle_refined_deg1.374
r_symmetry_vdw_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.11
r_dihedral_angle_3_deg13.471
r_dihedral_angle_4_deg13.3
r_mcangle_it8.464
r_mcbond_it5.765
r_dihedral_angle_1_deg4.296
r_scangle_it3.918
r_scbond_it2.44
r_angle_refined_deg1.374
r_symmetry_vdw_refined0.23
r_nbd_refined0.223
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.168
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4367
Nucleic Acid Atoms
Solvent Atoms573
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing