X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O4VPDB ENTRY 1o4v

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829814-16% (W/V) PEG 1000, 0.1 M MAGNESIUM CHLORIDE, 0.1 M IMIDAZOLE, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0339.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.47α = 90
b = 87.92β = 118.3
c = 86.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDNOIR-1ROSENBAUM-ROCK MONOCHROMATOR 1:HIGH-RESOLUTION DOUBLE-CRYSTAL SAGITTAL FOCUSING, ROSENBAUM-ROCK MONOCHROMATOR 2:DOUBLE CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR2006-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.24ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7419.799.50.05117.53.6112698112698
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.7999.50.5912.13.58305

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 1o4v1.7419.63106915106915565997.220.166780.165030.19974RANDOM17.646
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]
-5.041.71-0.565.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.381
r_dihedral_angle_3_deg14.264
r_dihedral_angle_4_deg12.408
r_dihedral_angle_1_deg5.748
r_scangle_it3.269
r_scbond_it2.158
r_angle_refined_deg1.547
r_mcangle_it1.232
r_angle_other_deg1.12
r_mcbond_it0.796
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.381
r_dihedral_angle_3_deg14.264
r_dihedral_angle_4_deg12.408
r_dihedral_angle_1_deg5.748
r_scangle_it3.269
r_scbond_it2.158
r_angle_refined_deg1.547
r_mcangle_it1.232
r_angle_other_deg1.12
r_mcbond_it0.796
r_mcbond_other0.269
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9455
Nucleic Acid Atoms
Solvent Atoms802
Heterogen Atoms8

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling