X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GFHPDB entry 3GFH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52982 M NaCl, 100 mM phosphate, 100 mM MES buffer, 5 % PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.415α = 90
b = 67.415β = 90
c = 79.604γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rSi III mirror2009-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.979464SSRLBL7-1

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
12.658.4398.90.1171.92.811274

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 3GFH2.658.381125097298.390.225230.221760.26672RANDOM34.034
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]
-34.58-34.5869.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.957
r_dihedral_angle_3_deg22.78
r_dihedral_angle_4_deg21.345
r_dihedral_angle_1_deg7.937
r_scangle_it3.633
r_scbond_it2.23
r_angle_refined_deg2.171
r_mcangle_it1.48
r_angle_other_deg0.866
r_mcbond_it0.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.957
r_dihedral_angle_3_deg22.78
r_dihedral_angle_4_deg21.345
r_dihedral_angle_1_deg7.937
r_scangle_it3.633
r_scbond_it2.23
r_angle_refined_deg2.171
r_mcangle_it1.48
r_angle_other_deg0.866
r_mcbond_it0.808
r_mcbond_other0.144
r_chiral_restr0.111
r_bond_refined_d0.023
r_gen_planes_refined0.015
r_bond_other_d0.002
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2942
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms9

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling