X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BITPDB ENTRY 2BIT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329130% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0138.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.374α = 90
b = 57.374β = 90
c = 87.384γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
10.9721.993.30.0768.2808927676718.118.1
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)
10.970.99565.90.2984

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 2BIT0.9721.858089276767405193.220.090.090710.089790.10845RANDOM7.44
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.639
r_dihedral_angle_4_deg17.186
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg6.57
r_sphericity_free6.337
r_sphericity_bonded2.251
r_scangle_it1.972
r_scbond_it1.621
r_angle_refined_deg1.571
r_mcangle_it1.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.639
r_dihedral_angle_4_deg17.186
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg6.57
r_sphericity_free6.337
r_sphericity_bonded2.251
r_scangle_it1.972
r_scbond_it1.621
r_angle_refined_deg1.571
r_mcangle_it1.314
r_mcbond_it1.087
r_angle_other_deg0.801
r_mcbond_other0.708
r_rigid_bond_restr0.693
r_nbd_other0.224
r_nbd_refined0.203
r_symmetry_vdw_other0.203
r_nbtor_refined0.196
r_xyhbond_nbd_refined0.174
r_symmetry_hbond_refined0.166
r_chiral_restr0.095
r_nbtor_other0.093
r_symmetry_vdw_refined0.085
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1240
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms6

Software

Software
Software NamePurpose
DNAdata collection
X-PLORmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing