X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AGPPDB entry 1AGP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.529120% PEG 3350, 0.2M Lithium citrate, pH 4.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2946.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.535α = 90
b = 118.275β = 90
c = 156.836γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2007-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

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
12.12099.80.1516.76.569383
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)
12.12.1799.40.9456.26812

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 1AGP2.272055104258999.5830.2150.2130.267Thin resolution shells23.166
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]
-0.9281.459-0.531
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.228
r_dihedral_angle_4_deg17.393
r_dihedral_angle_3_deg15.173
r_dihedral_angle_1_deg5.373
r_scangle_it3.392
r_mcangle_it3.197
r_scbond_it2.219
r_mcbond_it1.993
r_angle_other_deg1.823
r_angle_refined_deg1.423
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.228
r_dihedral_angle_4_deg17.393
r_dihedral_angle_3_deg15.173
r_dihedral_angle_1_deg5.373
r_scangle_it3.392
r_mcangle_it3.197
r_scbond_it2.219
r_mcbond_it1.993
r_angle_other_deg1.823
r_angle_refined_deg1.423
r_mcbond_other0.483
r_chiral_restr0.064
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7566
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms212

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction