X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V1D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298Tartrate 1-1.4 M, ADA 100 mM pH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.3782

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.368α = 90
b = 180.389β = 90
c = 235.422γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2014-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976256ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
13.350990.130.998.53.838276
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)
13.33.45990.81.23.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2V1D3.31503752874798.940.199060.198540.22324RANDOM108.238
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]
8.04-4.01-4.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.665
r_dihedral_angle_3_deg18.034
r_dihedral_angle_4_deg14.85
r_long_range_B_refined12.822
r_long_range_B_other12.821
r_mcangle_other9.754
r_mcangle_it9.753
r_scangle_other9.375
r_dihedral_angle_1_deg6.278
r_mcbond_it6.252
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.665
r_dihedral_angle_3_deg18.034
r_dihedral_angle_4_deg14.85
r_long_range_B_refined12.822
r_long_range_B_other12.821
r_mcangle_other9.754
r_mcangle_it9.753
r_scangle_other9.375
r_dihedral_angle_1_deg6.278
r_mcbond_it6.252
r_mcbond_other6.249
r_scbond_it5.734
r_scbond_other5.733
r_angle_refined_deg1.398
r_angle_other_deg0.942
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6303
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing