X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52932.5-2.7M ammonium sulfate, 0.1M sodium citrate (pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0960.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.781α = 90
b = 73.455β = 120.05
c = 81.251γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
11.765099.70.04820.13.865324
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)
11.761.821000.233.86506

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 REPLACEMENTTHROUGHOUT1AVD1.7634.9162003330899.50.186520.184440.22612RANDOM26.808
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.486
r_dihedral_angle_4_deg22.382
r_dihedral_angle_3_deg15.418
r_dihedral_angle_1_deg7.293
r_scangle_it6.326
r_scbond_it4.21
r_mcangle_it2.989
r_angle_refined_deg2.753
r_mcbond_it1.824
r_chiral_restr0.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.486
r_dihedral_angle_4_deg22.382
r_dihedral_angle_3_deg15.418
r_dihedral_angle_1_deg7.293
r_scangle_it6.326
r_scbond_it4.21
r_mcangle_it2.989
r_angle_refined_deg2.753
r_mcbond_it1.824
r_chiral_restr0.225
r_bond_refined_d0.034
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3811
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms190

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing