X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DMTPDB ENTRY 1DMT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION629430% Jeffamine D2001, 0.1M bis Tris, pH 6.0, VAPOR DIFFUSION, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.6553.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.88α = 90
b = 120.88β = 90
c = 192.346γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2005-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.382098.70.0713.7340993365611

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 1DMT2.38203188631886170599.050.266270.266270.262160.34506RANDOM45.686
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]
0.910.450.91-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_3_deg19.287
r_dihedral_angle_4_deg16.46
r_dihedral_angle_1_deg6.797
r_scangle_it2.151
r_angle_refined_deg1.525
r_scbond_it1.435
r_mcangle_it1.048
r_angle_other_deg0.893
r_mcbond_it0.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_3_deg19.287
r_dihedral_angle_4_deg16.46
r_dihedral_angle_1_deg6.797
r_scangle_it2.151
r_angle_refined_deg1.525
r_scbond_it1.435
r_mcangle_it1.048
r_angle_other_deg0.893
r_mcbond_it0.893
r_symmetry_hbond_refined0.374
r_metal_ion_refined0.272
r_nbd_refined0.22
r_symmetry_vdw_refined0.195
r_symmetry_vdw_other0.195
r_nbtor_refined0.191
r_xyhbond_nbd_refined0.19
r_nbd_other0.183
r_mcbond_other0.126
r_xyhbond_nbd_other0.116
r_chiral_restr0.09
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5305
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing