X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JBVPDB ENTRY 2JBV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629880 mM Nacacodylate and 150 mM Mg-Acetate at pH 6, with 20% v/v PEG6000 and 20% v/v glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.258α = 90
b = 346.029β = 94.33
c = 105.919γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 3152007-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12B1.0809NSLSX12B

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
12.475090.40.111146.2176109159203
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)
2.482.5750.30.2583.2

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 2JBV2.4729.99159203150964796690.780.231170.227890.29254RANDOM29.915
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]
0.14-0.02-0.13-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.454
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg18.816
r_dihedral_angle_1_deg7.092
r_scangle_it3.11
r_scbond_it1.917
r_angle_refined_deg1.667
r_mcangle_it1.204
r_mcbond_it0.645
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.454
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg18.816
r_dihedral_angle_1_deg7.092
r_scangle_it3.11
r_scbond_it1.917
r_angle_refined_deg1.667
r_mcangle_it1.204
r_mcbond_it0.645
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms32757
Nucleic Acid Atoms
Solvent Atoms325
Heterogen Atoms456

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling