X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DP0PDB entry 1DP0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5288PEG8000, NaCl, MgCl2, DTT, Bis-Tris, pH6.5, HANGING DROP AT 288K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.6653.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.23α = 90
b = 162.34β = 90
c = 202.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210KOHZU: Double Crystal SI(111)2008-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11589ALS8.3.1

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
1258.42870.1490.1985.23.2939519212019837.5
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)
2.72.8590.20.4080.5392.53.2258195

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 1DP0253.3829190112019841861000.181430.181410.180850.22042RANDOM24.347
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.823
r_dihedral_angle_4_deg14.535
r_dihedral_angle_3_deg12.425
r_dihedral_angle_1_deg5.694
r_scangle_it3.084
r_scbond_it1.993
r_mcangle_it1.585
r_angle_refined_deg0.971
r_mcbond_it0.903
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.823
r_dihedral_angle_4_deg14.535
r_dihedral_angle_3_deg12.425
r_dihedral_angle_1_deg5.694
r_scangle_it3.084
r_scbond_it1.993
r_mcangle_it1.585
r_angle_refined_deg0.971
r_mcbond_it0.903
r_nbtor_refined0.299
r_nbd_refined0.166
r_metal_ion_refined0.13
r_symmetry_vdw_refined0.123
r_symmetry_hbond_refined0.105
r_xyhbond_nbd_refined0.093
r_chiral_restr0.066
r_bond_refined_d0.006
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms32500
Nucleic Acid Atoms
Solvent Atoms3832
Heterogen Atoms580

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing