X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XAUpdb entry 1XAU and chain B from 1JMA
experimental modelPDB 1JMApdb entry 1XAU and chain B from 1JMA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62922.0 M NaFormate, 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.362

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.294α = 90
b = 167.116β = 90
c = 148.68γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.00ALS5.0.1

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
12.85099.90.0520.05213.43.981563915639-370
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)
12.82.91000.4550.4552.341543

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1XAU and chain B from 1JMA2.830-31559915591168699.950.23640.236490.231270.27838Thin shells61.821
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]
2.72-1.88-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.267
r_dihedral_angle_3_deg17.715
r_dihedral_angle_4_deg12.784
r_dihedral_angle_1_deg6.474
r_mcangle_it2.518
r_scangle_it2.308
r_mcbond_it1.909
r_scbond_it1.527
r_angle_refined_deg1.039
r_angle_other_deg0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.267
r_dihedral_angle_3_deg17.715
r_dihedral_angle_4_deg12.784
r_dihedral_angle_1_deg6.474
r_mcangle_it2.518
r_scangle_it2.308
r_mcbond_it1.909
r_scbond_it1.527
r_angle_refined_deg1.039
r_angle_other_deg0.68
r_mcbond_other0.283
r_symmetry_vdw_other0.226
r_nbtor_refined0.174
r_symmetry_vdw_refined0.172
r_nbd_refined0.171
r_nbd_other0.164
r_xyhbond_nbd_refined0.125
r_nbtor_other0.08
r_chiral_restr0.061
r_symmetry_hbond_refined0.033
r_bond_refined_d0.007
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3202
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing