X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5279.1535mM sodium acetate pH 4.6, 45 mM ADA, 30mM sodium chloride, 3-4 mM magnesium chloride, 3-3.5% PEG 4000, vapor diffusion, hanging drop, temperature 279.15K
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.459α = 90
b = 149.35β = 90
c = 79.584γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic Blue2005-04-27Molecular Replacement
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-002

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.5619.997.30.0414.5243699
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.561.6299.60.33.63.62

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 REPLACEMENTTHROUGHOUT1LZ71.5619.941471221797.290.190.18850.21725RANDOM20.931
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.962
r_dihedral_angle_4_deg19.426
r_dihedral_angle_3_deg12.762
r_dihedral_angle_1_deg6.77
r_scangle_it5.234
r_scbond_it3.505
r_mcangle_it2.288
r_angle_refined_deg2.247
r_mcbond_it1.396
r_chiral_restr0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.962
r_dihedral_angle_4_deg19.426
r_dihedral_angle_3_deg12.762
r_dihedral_angle_1_deg6.77
r_scangle_it5.234
r_scbond_it3.505
r_mcangle_it2.288
r_angle_refined_deg2.247
r_mcbond_it1.396
r_chiral_restr0.42
r_nbtor_refined0.314
r_symmetry_hbond_refined0.276
r_nbd_refined0.221
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.131
r_bond_refined_d0.03
r_gen_planes_refined0.013
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_refined
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 Atoms2185
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms71

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction