X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NXPPDB ID code: 3NXP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5295100 mM Tris-Hcl, pH 8.5 and 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6553.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.584α = 90
b = 103.136β = 90
c = 149.549γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
13.34096.90.185.43.91976819155-0.5-0.5
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)
13.33.3693.10.4492.12.8884

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 ID code: 3NXP3.340-0.5-0.5187521801198096.050.29630.294530.32878RANDOM58.389
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]
-3.433.78-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_3_deg19.687
r_dihedral_angle_4_deg15.785
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.225
r_scangle_it0.545
r_mcangle_it0.517
r_scbond_it0.305
r_mcbond_it0.286
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_3_deg19.687
r_dihedral_angle_4_deg15.785
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.225
r_scangle_it0.545
r_mcangle_it0.517
r_scbond_it0.305
r_mcbond_it0.286
r_chiral_restr0.081
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6884
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms56

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling