X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DV1PDB ENTRY 1DV1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M TRIS (PH 7.0); 0.2M MGCL2; 17-21% PEG3350
Crystal Properties
Matthews coefficientSolvent content
5.3776.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.402α = 90
b = 160.402β = 90
c = 146.764γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-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
12.5201000.0733.67.475554
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)
12.52.591000.374.77.3

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 1DV12.546.1371168376999.20.1980.1960.223RANDOM32.56
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]
0.520.260.52-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.593
r_dihedral_angle_4_deg17.158
r_dihedral_angle_3_deg13.867
r_dihedral_angle_1_deg5.811
r_scangle_it1.8
r_scbond_it1.195
r_angle_refined_deg1.083
r_angle_other_deg0.842
r_mcangle_it0.786
r_mcbond_it0.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.593
r_dihedral_angle_4_deg17.158
r_dihedral_angle_3_deg13.867
r_dihedral_angle_1_deg5.811
r_scangle_it1.8
r_scbond_it1.195
r_angle_refined_deg1.083
r_angle_other_deg0.842
r_mcangle_it0.786
r_mcbond_it0.723
r_symmetry_vdw_other0.224
r_nbd_refined0.199
r_nbd_other0.19
r_nbtor_refined0.168
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.12
r_symmetry_vdw_refined0.091
r_nbtor_other0.081
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms6731
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms10

Software

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