X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OGQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42910.2 M sodium malonate (pH 4.0), and 20% w/v polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.0439.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.895α = 90
b = 57.453β = 90
c = 135.538γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2017-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.978SSRFBL17U

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
12.35099.80.127188.813160
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)
12.32.360.491

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-VALUE1OGQ2.31137.4141384868899.390.1650.16220.222838.373
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]
0.107-1.1661.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.238
r_dihedral_angle_4_deg21.527
r_dihedral_angle_3_deg16.941
r_dihedral_angle_1_deg7.722
r_lrange_other5.642
r_lrange_it5.64
r_scangle_it4.314
r_scangle_other4.313
r_scbond_it2.755
r_scbond_other2.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.238
r_dihedral_angle_4_deg21.527
r_dihedral_angle_3_deg16.941
r_dihedral_angle_1_deg7.722
r_lrange_other5.642
r_lrange_it5.64
r_scangle_it4.314
r_scangle_other4.313
r_scbond_it2.755
r_scbond_other2.755
r_mcangle_it2.483
r_mcangle_other2.482
r_angle_refined_deg2.047
r_mcbond_it1.66
r_mcbond_other1.659
r_angle_other_deg1.371
r_symmetry_nbd_refined0.266
r_symmetry_xyhbond_nbd_refined0.243
r_nbd_other0.233
r_nbd_refined0.208
r_symmetry_nbd_other0.196
r_xyhbond_nbd_refined0.192
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_other0.142
r_xyhbond_nbd_other0.126
r_chiral_restr0.09
r_symmetry_nbtor_other0.088
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2413
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms28

Software

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