X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AE1PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental modelPDB 1AE1PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental modelPDB 2EW8PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental modelPDB 1ZEMPDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental modelPDB 1AHHPDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental modelPDB 1VL8PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52932.4M Na Malonate pH 7.0, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.225α = 90
b = 87.854β = 90
c = 100.583γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCOSMIC2007-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.822.2199.80.0560.06517.83.991682914992
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)
11.81.91000.5670.6623.812938

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 entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL81.822.2122214120399.680.158810.156810.19719RANDOM29.684
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]
0.38-1.290.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.662
r_dihedral_angle_4_deg14.306
r_dihedral_angle_3_deg10.488
r_scangle_it6.621
r_dihedral_angle_1_deg5.596
r_scbond_it4.712
r_mcangle_it3.306
r_mcbond_it2.318
r_angle_refined_deg1.213
r_angle_other_deg0.918
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.662
r_dihedral_angle_4_deg14.306
r_dihedral_angle_3_deg10.488
r_scangle_it6.621
r_dihedral_angle_1_deg5.596
r_scbond_it4.712
r_mcangle_it3.306
r_mcbond_it2.318
r_angle_refined_deg1.213
r_angle_other_deg0.918
r_mcbond_other0.71
r_symmetry_vdw_other0.248
r_nbd_refined0.235
r_nbd_other0.189
r_nbtor_refined0.173
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.151
r_symmetry_hbond_refined0.13
r_nbtor_other0.086
r_chiral_restr0.076
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1748
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing