X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V0DPDB: 3V0D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827717.5-22.5% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0; crystals were dehydrated in 30% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2946.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.863α = 86.55
b = 83.863β = 89.55
c = 83.604γ = 89.38
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rDouble Crystal Si(111)2010-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1158ALS8.3.1

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
11.583.880.50.05515.32.622043817665922
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)
11.51.583.10.292.41.4

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: 3V0D1.683.71172685138269743880.070.258090.255920.29839RANDOM24.766
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]
-1.960.420.340.59-0.151.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.908
r_dihedral_angle_4_deg14.698
r_dihedral_angle_3_deg13.28
r_dihedral_angle_1_deg5.286
r_scangle_it1.268
r_angle_refined_deg0.956
r_scbond_it0.806
r_mcangle_it0.68
r_mcbond_it0.378
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.908
r_dihedral_angle_4_deg14.698
r_dihedral_angle_3_deg13.28
r_dihedral_angle_1_deg5.286
r_scangle_it1.268
r_angle_refined_deg0.956
r_scbond_it0.806
r_mcangle_it0.68
r_mcbond_it0.378
r_chiral_restr0.066
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10548
Nucleic Acid Atoms
Solvent Atoms1169
Heterogen Atoms45

Software

Software
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling