X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RDUPDB ENTRY 3RDU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52980.1 M Na acetate, pH 4.5, 3 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.25α = 90
b = 81.64β = 90
c = 84.537γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
12.15099.90.0997.46.316282
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)
12.12.1499.60.8185.6795

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 3RDU2.10119.811619781799.360.21560.21250.2777RANDOM22.1929
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]
-0.04-0.020.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.242
r_dihedral_angle_3_deg16.005
r_dihedral_angle_4_deg14.594
r_scbond_it7.558
r_dihedral_angle_1_deg7.189
r_mcangle_it4.006
r_angle_refined_deg1.385
r_rigid_bond_restr1.36
r_scangle_it1.325
r_mcbond_it1.277
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.242
r_dihedral_angle_3_deg16.005
r_dihedral_angle_4_deg14.594
r_scbond_it7.558
r_dihedral_angle_1_deg7.189
r_mcangle_it4.006
r_angle_refined_deg1.385
r_rigid_bond_restr1.36
r_scangle_it1.325
r_mcbond_it1.277
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1819
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms6

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction