X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BL3PDB ENTRY 1bl3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.4M SODIUM CITRATE, 50mM HEPES PH 7.5, 7.5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5952.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.327α = 90
b = 72.909β = 108.6
c = 79.851γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.94937APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.975.699.520.0510.05117.53.7426744246922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9299.60.2990.2992.5

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 1bl31.975.594246940326214399.520.19580.19760.195780.23202RANDOM27.056
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]
1.770.55-0.04-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.579
r_dihedral_angle_4_deg14.37
r_dihedral_angle_3_deg13.052
r_dihedral_angle_1_deg4.949
r_scangle_it4.535
r_angle_other_deg4.118
r_scbond_it3.004
r_mcangle_it2.141
r_mcbond_it1.243
r_angle_refined_deg1.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.579
r_dihedral_angle_4_deg14.37
r_dihedral_angle_3_deg13.052
r_dihedral_angle_1_deg4.949
r_scangle_it4.535
r_angle_other_deg4.118
r_scbond_it3.004
r_mcangle_it2.141
r_mcbond_it1.243
r_angle_refined_deg1.144
r_nbd_other0.255
r_symmetry_vdw_other0.232
r_nbd_refined0.213
r_nbtor_refined0.187
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.138
r_symmetry_vdw_refined0.112
r_nbtor_other0.11
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_other0.005
r_gen_planes_refined0.003
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms3419
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms11

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling