X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62957,5% Na malonate, 20mM AcNa, 100 mM glycine, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3748.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.47α = 90
b = 57.55β = 90
c = 101.39γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2005-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
11.920.6490.70.1610.0728.212.4721425
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)
11.92.0183.80.5110.3272.342.383129

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1SHG1.920.6421425114697.640.215240.215240.21270.26411RANDOM25.629
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]
-0.070.21-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.382
r_dihedral_angle_3_deg18.855
r_sphericity_bonded15.262
r_dihedral_angle_4_deg15.084
r_sphericity_free9.796
r_dihedral_angle_1_deg5.681
r_scangle_it4.927
r_scbond_it3.452
r_mcangle_it2.806
r_rigid_bond_restr2.492
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.382
r_dihedral_angle_3_deg18.855
r_sphericity_bonded15.262
r_dihedral_angle_4_deg15.084
r_sphericity_free9.796
r_dihedral_angle_1_deg5.681
r_scangle_it4.927
r_scbond_it3.452
r_mcangle_it2.806
r_rigid_bond_restr2.492
r_mcbond_it1.799
r_angle_refined_deg1.535
r_nbtor_refined0.312
r_nbd_refined0.211
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.129
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2144
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing