X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M2TPDB ENTRY 1M2T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2.5293pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.5873.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.059α = 90
b = 107.059β = 90
c = 312.375γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.791.290.60.4733.66.33032722
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)
12.72.751000.060.473.66.3

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 1M2T2.719.7428628147099.970.228210.226220.26704RANDOM46.964
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]
1.830.921.83-2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.411
r_dihedral_angle_3_deg16.934
r_dihedral_angle_4_deg13.516
r_dihedral_angle_1_deg6.906
r_scangle_it2.053
r_angle_refined_deg1.34
r_scbond_it1.275
r_mcangle_it0.987
r_mcbond_it0.542
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.411
r_dihedral_angle_3_deg16.934
r_dihedral_angle_4_deg13.516
r_dihedral_angle_1_deg6.906
r_scangle_it2.053
r_angle_refined_deg1.34
r_scbond_it1.275
r_mcangle_it0.987
r_mcbond_it0.542
r_nbtor_refined0.314
r_symmetry_vdw_refined0.256
r_nbd_refined0.214
r_xyhbond_nbd_refined0.121
r_symmetry_hbond_refined0.113
r_chiral_restr0.092
r_gen_planes_refined0.05
r_bond_refined_d0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3911
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing