X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D66pdb entry 3D66

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION627716-18% PEG 3000, 0.18-0.22mM Na/K-tartrate, 50mM L-glutamate, 50mM L-arginine, 1mM GEMSA, pH 6.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5665.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.05α = 90
b = 161.05β = 90
c = 138.99γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97320ESRFID23-1

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
13.449.2799.60.09111.44.92892028900-3.7
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)
13.43.581000.632.25

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3D663.444.092742427424147299.570.200430.197720.25218RANDOM100.733
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]
4.122.064.12-6.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.753
r_dihedral_angle_3_deg20.197
r_dihedral_angle_4_deg17.8
r_dihedral_angle_1_deg8.742
r_angle_refined_deg1.485
r_scangle_it1.407
r_angle_other_deg0.945
r_scbond_it0.872
r_mcangle_it0.836
r_mcbond_it0.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.753
r_dihedral_angle_3_deg20.197
r_dihedral_angle_4_deg17.8
r_dihedral_angle_1_deg8.742
r_angle_refined_deg1.485
r_scangle_it1.407
r_angle_other_deg0.945
r_scbond_it0.872
r_mcangle_it0.836
r_mcbond_it0.471
r_metal_ion_refined0.353
r_nbd_refined0.237
r_symmetry_vdw_other0.207
r_nbtor_refined0.201
r_nbd_other0.196
r_xyhbond_nbd_refined0.175
r_symmetry_vdw_refined0.168
r_nbtor_other0.096
r_symmetry_hbond_refined0.092
r_chiral_restr0.086
r_mcbond_other0.059
r_xyhbond_nbd_other0.017
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.003
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9738
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
SCALAdata scaling
PHASERphasing