X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.52940.1 M sodium citrate, 16 % polyethylene glycol 6000, 5% isopropanol, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0640.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.4α = 90
b = 56.4β = 90
c = 39.4γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 225 mm2005-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.75APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.1228.299.30.0510.05152.912.24118411828
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.2930.1410.14112.510.9386

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 REPLACEMENTTHROUGHOUT1CDQ2.1228.24115411518999.280.180.180.1770.254RANDOM22.672
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]
-0.95-0.48-0.951.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.237
r_dihedral_angle_4_deg16.183
r_dihedral_angle_3_deg15.533
r_dihedral_angle_1_deg7.224
r_scangle_it2.77
r_scbond_it1.694
r_angle_refined_deg1.44
r_mcangle_it0.996
r_mcbond_it0.505
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.237
r_dihedral_angle_4_deg16.183
r_dihedral_angle_3_deg15.533
r_dihedral_angle_1_deg7.224
r_scangle_it2.77
r_scbond_it1.694
r_angle_refined_deg1.44
r_mcangle_it0.996
r_mcbond_it0.505
r_nbtor_refined0.3
r_nbd_refined0.217
r_symmetry_hbond_refined0.205
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.18
r_chiral_restr0.097
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms608
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing