X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5292Protein: 9.8 mg/ml, 0.01M Tris-HCl pH 8.3, Screen: PACT (F6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1342.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.745α = 90
b = 184.745β = 90
c = 48.761γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.55301000.10.10.1060.03520.59.8138516-312.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.581000.7110.7110.7570.2580.8613.28.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4QRJ1.5529.33131376694599.980.127210.125690.15552RANDOM12.521
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]
0.070.040.07-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.869
r_dihedral_angle_4_deg17.193
r_dihedral_angle_3_deg10.217
r_dihedral_angle_1_deg5.515
r_long_range_B_refined4.998
r_long_range_B_other4.513
r_scangle_other3.337
r_scbond_it2.187
r_scbond_other2.187
r_mcangle_it1.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.869
r_dihedral_angle_4_deg17.193
r_dihedral_angle_3_deg10.217
r_dihedral_angle_1_deg5.515
r_long_range_B_refined4.998
r_long_range_B_other4.513
r_scangle_other3.337
r_scbond_it2.187
r_scbond_other2.187
r_mcangle_it1.426
r_mcangle_other1.426
r_angle_refined_deg1.376
r_mcbond_it0.97
r_mcbond_other0.97
r_angle_other_deg0.449
r_chiral_restr0.07
r_gen_planes_refined0.042
r_gen_planes_other0.039
r_bond_refined_d0.008
r_bond_other_d0.001
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 Atoms7698
Nucleic Acid Atoms
Solvent Atoms1779
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing