X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QCTPDB ENTRY 3QCT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62940.095 M sodium citrate pH 5.6, 19% (v/v) isopropanol, 19% (w/v) PEG 4000, and 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.7154.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.526α = 90
b = 184.351β = 90
c = 130γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0000NSLSX25

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
11.97946.74999.90.06112.27.472518-3
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)
1.9792.0199.90.4827.23613

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 3QCT1.97946.7497256872488365399.890.2230.2230.22150.2516RANDOM34.587
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]
-0.46-0.510.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.781
r_dihedral_angle_4_deg22.426
r_dihedral_angle_3_deg13.692
r_dihedral_angle_1_deg6.374
r_scangle_it2.757
r_scbond_it1.713
r_angle_refined_deg1.288
r_mcangle_it1.144
r_mcbond_it0.619
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.781
r_dihedral_angle_4_deg22.426
r_dihedral_angle_3_deg13.692
r_dihedral_angle_1_deg6.374
r_scangle_it2.757
r_scbond_it1.713
r_angle_refined_deg1.288
r_mcangle_it1.144
r_mcbond_it0.619
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6686
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms50

Software

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