X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NV1PDB ENTRY 4NV1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5289MytuD.17389.a.A1.PW30616 at 19 mg/mL against JCSG+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 supplemented with 25% ethylene glycol, crystal tracking ID 220349d6, unique puck ID bdu3-7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5551.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.08α = 90
b = 136.45β = 103.74
c = 99.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.15099.80.0615.223.8128170-340.095
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)
12.152.2199.90.4622.97

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4NV12.120128170653599.760.18890.18670.231RANDOM40.346
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]
0.230.3-0.25-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.963
r_dihedral_angle_4_deg20.101
r_dihedral_angle_3_deg12.906
r_dihedral_angle_1_deg5.741
r_mcangle_it2.012
r_scbond_it1.962
r_angle_refined_deg1.422
r_mcbond_it1.311
r_chiral_restr0.092
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.963
r_dihedral_angle_4_deg20.101
r_dihedral_angle_3_deg12.906
r_dihedral_angle_1_deg5.741
r_mcangle_it2.012
r_scbond_it1.962
r_angle_refined_deg1.422
r_mcbond_it1.311
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14616
Nucleic Acid Atoms
Solvent Atoms973
Heterogen Atoms88

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction