X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52937% PEG 8000, 0.1 M MES buffer, pH 6.5, 20% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.3347.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.07α = 90
b = 65.897β = 101.35
c = 54.642γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.67150.198.20.0290.0350.01920.8335715
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)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6711.7391.20.30.30.3770.2242.62.4

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 REPLACEMENTTHROUGHOUT1NVR1.750.0132388171098.620.15850.15650.1971RANDOM34.655
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]
-1.47-0.96-0.081.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.144
r_dihedral_angle_4_deg20.669
r_dihedral_angle_3_deg16.274
r_dihedral_angle_1_deg5.336
r_angle_refined_deg2.195
r_angle_other_deg1.142
r_chiral_restr0.144
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.144
r_dihedral_angle_4_deg20.669
r_dihedral_angle_3_deg16.274
r_dihedral_angle_1_deg5.336
r_angle_refined_deg2.195
r_angle_other_deg1.142
r_chiral_restr0.144
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2097
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms31

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata processing
MOLREPphasing