X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RDMPDB ENTRY 3RDM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529810% PEG1000, 10% PEG8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9837.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.354α = 90
b = 57.354β = 90
c = 76.839γ = 90
Symmetry
Space GroupP 42 21 2

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 X29A0.9791NSLSX29A

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
11.55099.70.07114.16.821154
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)
11.51.5399.90.5737.21023

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 3RDM1.52021100108999.670.17140.16960.2071RANDOM16.5569
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]
-0.71-0.711.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.483
r_dihedral_angle_4_deg11.689
r_dihedral_angle_3_deg9.291
r_dihedral_angle_1_deg6.632
r_scbond_it4.023
r_mcangle_it2.705
r_scangle_it1.628
r_angle_refined_deg1.373
r_mcbond_it1.286
r_rigid_bond_restr0.866
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.483
r_dihedral_angle_4_deg11.689
r_dihedral_angle_3_deg9.291
r_dihedral_angle_1_deg6.632
r_scbond_it4.023
r_mcangle_it2.705
r_scangle_it1.628
r_angle_refined_deg1.373
r_mcbond_it1.286
r_rigid_bond_restr0.866
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms905
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms34

Software

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