X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CVH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.2 M Ammonium sulfate, 30 % w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3647.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.461α = 90
b = 63.25β = 108.44
c = 58.672γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray88PIXELDECTRIS EIGER2 X 16M2021-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.4855.6699.80.0770.0790.01911817.166333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.5699.34.0274.1541.010.40916.6

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 REPLACEMENTTHROUGHOUT5CVH1.4855.6662522344299.180.18090.17970.2037RANDOM33.211
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]
1.20.040.06-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.302
r_dihedral_angle_4_deg17.253
r_dihedral_angle_3_deg14.298
r_dihedral_angle_1_deg6.94
r_angle_refined_deg1.672
r_angle_other_deg1.378
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.302
r_dihedral_angle_4_deg17.253
r_dihedral_angle_3_deg14.298
r_dihedral_angle_1_deg6.94
r_angle_refined_deg1.672
r_angle_other_deg1.378
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2865
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms49

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction