X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AGIPDB ENTRY 4AGI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1200 MM CACL2, 25% PEG 4K AND 100 MM TRIS, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.243.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.03α = 90
b = 70.44β = 108.34
c = 117.8γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.7534.4497.10.08123.7121067213.9
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)
11.751.8596.10.393.23.7

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 4AGI1.76111.82114970607897.30.154930.153740.1778RANDOM17.275
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]
-0.910.81-1.411.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.946
r_dihedral_angle_4_deg15.23
r_dihedral_angle_3_deg11.926
r_dihedral_angle_1_deg7.536
r_mcangle_it1.619
r_angle_refined_deg1.455
r_scbond_it1.442
r_mcbond_it1.013
r_mcbond_other1.013
r_angle_other_deg0.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.946
r_dihedral_angle_4_deg15.23
r_dihedral_angle_3_deg11.926
r_dihedral_angle_1_deg7.536
r_mcangle_it1.619
r_angle_refined_deg1.455
r_scbond_it1.442
r_mcbond_it1.013
r_mcbond_other1.013
r_angle_other_deg0.779
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9753
Nucleic Acid Atoms
Solvent Atoms1060
Heterogen Atoms454

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing