X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DHTPDB ENTRY 3dht

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529350mM phosphate buffer, peg 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3547.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.14α = 90
b = 54.015β = 93.8
c = 115.008γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray273IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54170

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
12.73097.40.12624.22.8315682
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.899.10.31981.22.681549

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 3dht2.719.1614091155997.570.219060.213010.27497RANDOM23.491
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_3_deg18.002
r_dihedral_angle_4_deg6.43
r_dihedral_angle_1_deg4.782
r_angle_refined_deg1.028
r_scangle_it0.648
r_mcangle_it0.435
r_scbond_it0.39
r_nbtor_refined0.287
r_mcbond_it0.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_3_deg18.002
r_dihedral_angle_4_deg6.43
r_dihedral_angle_1_deg4.782
r_angle_refined_deg1.028
r_scangle_it0.648
r_mcangle_it0.435
r_scbond_it0.39
r_nbtor_refined0.287
r_mcbond_it0.239
r_symmetry_vdw_refined0.23
r_nbd_refined0.188
r_chiral_restr0.15
r_xyhbond_nbd_refined0.121
r_symmetry_hbond_refined0.101
r_metal_ion_refined0.025
r_bond_refined_d0.006
r_gen_planes_refined0.002
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_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 Atoms4368
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms172

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
AUTOMARdata reduction