X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TM3PDB Entry 1TM3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6277sodium citrate, isopropanol, PEG 4000, xylitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.463.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.72α = 90
b = 93.72β = 90
c = 185.853γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.0ALS8.3.1

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
11.781.6598.20.06813.94.85279152791-3-3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 1TM31.781.65-3-35278850141264798.160.152410.152410.150850.18168inherited from PDB entry 1TM318.044
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]
0.140.070.14-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.818
r_scangle_it4.528
r_scbond_it2.719
r_angle_refined_deg1.8
r_mcangle_it1.581
r_mcbond_it0.939
r_symmetry_vdw_refined0.4
r_nbd_refined0.216
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.818
r_scangle_it4.528
r_scbond_it2.719
r_angle_refined_deg1.8
r_mcangle_it1.581
r_mcbond_it0.939
r_symmetry_vdw_refined0.4
r_nbd_refined0.216
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.167
r_chiral_restr0.135
r_metal_ion_refined0.077
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2560
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
TRUNCATEdata scaling
EPMRphasing