X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DB3PDB ENTRY 2DB3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.
Crystal Properties
Matthews coefficientSolvent content
2.0434

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.438α = 90
b = 61.032β = 101.67
c = 89.111γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDMIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.98793.20.0815.033.11059821
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)
11.91.9772.20.332.532.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2DB31.9134.5323631704930.2010.1980.255RANDOM27.07
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]
0.16-0.16-0.280.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.625
r_dihedral_angle_4_deg17.517
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg6.037
r_scangle_it4.791
r_scbond_it3.122
r_mcangle_it1.889
r_angle_refined_deg1.682
r_mcbond_it1.209
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.625
r_dihedral_angle_4_deg17.517
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg6.037
r_scangle_it4.791
r_scbond_it3.122
r_mcangle_it1.889
r_angle_refined_deg1.682
r_mcbond_it1.209
r_nbtor_refined0.312
r_symmetry_hbond_refined0.251
r_nbd_refined0.227
r_symmetry_vdw_refined0.222
r_xyhbond_nbd_refined0.181
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3727
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms

Software

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