X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VE6PDB ENTRY 1VE6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529378mM sodium acetate, 0.44mM EDTA, 2.2% PEG 4000, 0.56% beta-octyl-glucoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.682α = 90
b = 103.989β = 90
c = 168.594γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIC2005-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
1219.53794.80.11513.0776464-3
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)
122.180.20.3833.18216

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VE62.0119.526807968079360294.750.177610.177610.175540.21693RANDOM (AS FOR RELATED PDB ENTRY 2HU5)17.854
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]
-0.07-0.060.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.421
r_scangle_it1.968
r_mcangle_it1.747
r_angle_refined_deg1.274
r_scbond_it1.21
r_mcbond_it1.087
r_angle_other_deg0.838
r_symmetry_vdw_refined0.266
r_nbd_other0.248
r_symmetry_vdw_other0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.421
r_scangle_it1.968
r_mcangle_it1.747
r_angle_refined_deg1.274
r_scbond_it1.21
r_mcbond_it1.087
r_angle_other_deg0.838
r_symmetry_vdw_refined0.266
r_nbd_other0.248
r_symmetry_vdw_other0.248
r_nbd_refined0.195
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.147
r_chiral_restr0.086
r_nbtor_other0.085
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8623
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing