X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GD7PDB entry 1GD7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2940.1 M Potassium dihydrogen phosphate, 12% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.5265.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.432α = 90
b = 148.432β = 90
c = 54.054γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray102IMAGE PLATERIGAKU RAXIS IVVariMax Cu HF2006-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54178

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
1228.0598.60.04420.44.5847258456755
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)
122.07970.314.64.254438

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 1GD7228.054567445674231198.530.1920.1920.190.23RANDOM18.691
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]
0.70.350.7-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.857
r_dihedral_angle_4_deg23.347
r_dihedral_angle_3_deg16.635
r_dihedral_angle_1_deg6.969
r_scangle_it3.968
r_scbond_it2.409
r_angle_refined_deg1.777
r_mcangle_it1.254
r_mcbond_it0.783
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.857
r_dihedral_angle_4_deg23.347
r_dihedral_angle_3_deg16.635
r_dihedral_angle_1_deg6.969
r_scangle_it3.968
r_scbond_it2.409
r_angle_refined_deg1.777
r_mcangle_it1.254
r_mcbond_it0.783
r_nbtor_refined0.309
r_xyhbond_nbd_refined0.286
r_symmetry_hbond_refined0.225
r_nbd_refined0.204
r_symmetry_vdw_refined0.19
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3306
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms36

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing