X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D9SPDB ENTRY 3D9S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.9281RESERVOIR SOLUTION (100MM TRIS-HCL PH7.9, 100MM NACL, 21% PEG400) MIXED WITH EACH OF 1,6-HEXANEDIOL (30%, V/V) AND 1,3-PROPANEDIOL (40%, V/V) AND MIXED WITH THE TEMPERATURE 281K
Crystal Properties
Matthews coefficientSolvent content
3.8768.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.75α = 90
b = 170.75β = 90
c = 189.671γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
12.650.8198.80.180.1567494885238
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)
12.62.7499.40.7780.6712.14

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 3D9S2.650.894885475498.80.1950.1930.23RANDOM32.03
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]
1.070.531.07-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.31
r_dihedral_angle_4_deg13.234
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg4.307
r_scangle_it1.018
r_angle_refined_deg0.95
r_scbond_it0.603
r_mcangle_it0.564
r_mcbond_it0.313
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.31
r_dihedral_angle_4_deg13.234
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg4.307
r_scangle_it1.018
r_angle_refined_deg0.95
r_scbond_it0.603
r_mcangle_it0.564
r_mcbond_it0.313
r_nbtor_refined0.3
r_symmetry_vdw_refined0.19
r_nbd_refined0.188
r_symmetry_hbond_refined0.184
r_xyhbond_nbd_refined0.102
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14447
Nucleic Acid Atoms
Solvent Atoms796
Heterogen Atoms56

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement