X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y23PDB entry 1Y23

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6289JCSG A4; 30 % MPD, 0.1 M ACETATE PH 4.6, 20 MM CACL2, MYSMA.00754.A.A1 AT 19.9 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1943.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.15α = 90
b = 63.52β = 100.51
c = 76.5γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSATURN2010-07-07MSINGLE 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)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
11.935.2795.50.0423.013.52206721077-320.17
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9580.54.91.7

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 DIFFRACTIONMRTHROUGHOUTPDB entry 1Y231.935.27220672105310620.1590.1590.1570.191RANDOM14.73
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]
-0.74-0.191.67-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.919
r_dihedral_angle_4_deg19.837
r_dihedral_angle_3_deg11.911
r_dihedral_angle_1_deg6.179
r_scangle_it2.639
r_scbond_it1.637
r_angle_refined_deg1.362
r_mcangle_it0.97
r_angle_other_deg0.875
r_mcbond_it0.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.919
r_dihedral_angle_4_deg19.837
r_dihedral_angle_3_deg11.911
r_dihedral_angle_1_deg6.179
r_scangle_it2.639
r_scbond_it1.637
r_angle_refined_deg1.362
r_mcangle_it0.97
r_angle_other_deg0.875
r_mcbond_it0.529
r_mcbond_other0.12
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms2044
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms60

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling