X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VD5PDB ENTRY 2VD5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.627710-20% PEG 3350, 0.1 M BISTRIS, 0.1 M SODIUM TARTRATE, 0.1 M AMMONIUM SULPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, VAPOR DIFFUSION, SITTING DROP, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.3246.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.95α = 90
b = 123.52β = 101.13
c = 84.77γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.92DiamondI04

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
12.1549.5997.10.116478544551522
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)
12.152.2184.30.467

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 2VD52.154014785445515241297.30.2230.2210.273RANDOM40.216
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]
-1.580.8-1.553.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.678
r_dihedral_angle_3_deg18.052
r_dihedral_angle_4_deg17.948
r_dihedral_angle_1_deg7.056
r_scangle_it4.499
r_scbond_it2.895
r_angle_refined_deg2.009
r_mcangle_it1.793
r_mcbond_it0.983
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.678
r_dihedral_angle_3_deg18.052
r_dihedral_angle_4_deg17.948
r_dihedral_angle_1_deg7.056
r_scangle_it4.499
r_scbond_it2.895
r_angle_refined_deg2.009
r_mcangle_it1.793
r_mcbond_it0.983
r_chiral_restr0.136
r_bond_refined_d0.022
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6225
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms88

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling