X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PINPDB ENTRY 1PIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52931.8M Ammonium citrate, 0.1M Tris buffer, 5mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.064α = 90
b = 36.576β = 101.11
c = 51.328γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2005-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.929.589.10.0626.12.6153691536911
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)
1.91.97920.3232.11.8587

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PIN229.49132401324072694.120.171680.171680.167530.24876RANDOM24.902
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]
-0.04-0.11-0.050.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.358
r_dihedral_angle_4_deg18.053
r_dihedral_angle_3_deg15.858
r_dihedral_angle_1_deg7.427
r_scangle_it4.846
r_scbond_it3.173
r_mcangle_it1.834
r_angle_refined_deg1.805
r_mcbond_it1.073
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.358
r_dihedral_angle_4_deg18.053
r_dihedral_angle_3_deg15.858
r_dihedral_angle_1_deg7.427
r_scangle_it4.846
r_scbond_it3.173
r_mcangle_it1.834
r_angle_refined_deg1.805
r_mcbond_it1.073
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1795
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms28

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling