X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OIBPDB ENTRY 2OIB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72932.3M sodium malonate, 0.1M sodium acetate, 0.01M DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.894α = 90
b = 141.321β = 122.27
c = 88.263γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 2102005-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.0ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45099.67.1163.762496358.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4996.70.5112.12.96058

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 DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUTPDB ENTRY 2OIB2.448.1759030314799.860.225670.222850.2781RANDOM64.797
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]
3.211.11-0.87-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.937
r_dihedral_angle_4_deg22.439
r_dihedral_angle_3_deg16.899
r_dihedral_angle_1_deg5.516
r_scangle_it2.304
r_angle_refined_deg1.762
r_scbond_it1.347
r_mcangle_it1.302
r_mcbond_it0.732
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.937
r_dihedral_angle_4_deg22.439
r_dihedral_angle_3_deg16.899
r_dihedral_angle_1_deg5.516
r_scangle_it2.304
r_angle_refined_deg1.762
r_scbond_it1.347
r_mcangle_it1.302
r_mcbond_it0.732
r_nbtor_refined0.298
r_symmetry_hbond_refined0.25
r_nbd_refined0.2
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.152
r_chiral_restr0.141
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8893
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling