X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSSPDB ENTRY 2OSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82933.6M Na formate, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.014α = 90
b = 47.442β = 90
c = 78.024γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

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
11.5519.699.40.07615.351886518865-3-325.811
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)
11.551.699.50.4095.1

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 2OSS1.5519.6188651885596199.450.1840.1860.1840.219RANDOM18.5
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]
6.28-3.57-2.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_sphericity_free14.672
r_dihedral_angle_4_deg14.272
r_dihedral_angle_3_deg13.267
r_sphericity_bonded9.737
r_scangle_it6.295
r_dihedral_angle_1_deg5.823
r_scbond_it4.944
r_mcangle_it3.598
r_rigid_bond_restr3.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_sphericity_free14.672
r_dihedral_angle_4_deg14.272
r_dihedral_angle_3_deg13.267
r_sphericity_bonded9.737
r_scangle_it6.295
r_dihedral_angle_1_deg5.823
r_scbond_it4.944
r_mcangle_it3.598
r_rigid_bond_restr3.312
r_mcbond_it2.9
r_angle_refined_deg2.239
r_mcbond_other1.754
r_angle_other_deg1.227
r_xyhbond_nbd_refined0.275
r_symmetry_vdw_other0.269
r_nbd_refined0.231
r_nbtor_refined0.196
r_nbd_other0.188
r_chiral_restr0.152
r_symmetry_hbond_refined0.148
r_symmetry_vdw_refined0.138
r_nbtor_other0.104
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1036
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms10

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
MOLREPphasing