X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RDHPDB ENTRIES 2RDH and 2Z8L
experimental modelPDB 2Z8LPDB ENTRIES 2RDH and 2Z8L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291.1521% MPEG 5000, 0.2M bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
2.346.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.102α = 90
b = 81.195β = 105.45
c = 57.301γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2010-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.727.6299.70.05817.149.94643528.8
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)
11.71.7899.20.6989.66696

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 ENTRIES 2RDH and 2Z8L1.727.6244078234599.550.211260.208640.2614RANDOM29.686
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]
-1.98-1.720.910.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.412
r_dihedral_angle_4_deg20.408
r_dihedral_angle_3_deg14.348
r_dihedral_angle_1_deg5.9
r_scangle_it5.554
r_scbond_it3.423
r_mcangle_it2.353
r_angle_refined_deg2.096
r_mcbond_it1.407
r_chiral_restr0.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.412
r_dihedral_angle_4_deg20.408
r_dihedral_angle_3_deg14.348
r_dihedral_angle_1_deg5.9
r_scangle_it5.554
r_scbond_it3.423
r_mcangle_it2.353
r_angle_refined_deg2.096
r_mcbond_it1.407
r_chiral_restr0.157
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms3108
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms10

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling