X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YPV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Calcium chloride, Bis-Tris, PEG MME 550, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.8868.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.394α = 90
b = 129.786β = 90
c = 220.582γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 315r2017-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97776SSRFBL19U1

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
11.99648.70199.810.10742.63313.213695331.7
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)
122.0710.357

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4YPV1.99648.701136861677799.8190.160.15890.189432.316
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]
0.035-0.029-0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.575
r_dihedral_angle_4_deg23.875
r_dihedral_angle_3_deg12.399
r_dihedral_angle_1_deg6.613
r_lrange_it6.509
r_lrange_other6.448
r_scangle_it5.14
r_scangle_other5.14
r_scbond_it3.829
r_scbond_other3.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.575
r_dihedral_angle_4_deg23.875
r_dihedral_angle_3_deg12.399
r_dihedral_angle_1_deg6.613
r_lrange_it6.509
r_lrange_other6.448
r_scangle_it5.14
r_scangle_other5.14
r_scbond_it3.829
r_scbond_other3.829
r_mcangle_other3.519
r_mcangle_it3.517
r_mcbond_it3.085
r_mcbond_other3.065
r_angle_refined_deg1.738
r_angle_other_deg1.461
r_nbd_refined0.21
r_symmetry_xyhbond_nbd_refined0.207
r_xyhbond_nbd_refined0.202
r_symmetry_nbd_other0.179
r_nbd_other0.176
r_nbtor_refined0.168
r_symmetry_xyhbond_nbd_other0.157
r_chiral_restr0.092
r_symmetry_nbtor_other0.083
r_symmetry_nbd_refined0.081
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9125
Nucleic Acid Atoms
Solvent Atoms1429
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing