X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OI2pdb entry 1OI2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629520% PEG 8000, 0.1M Sodium Citrate pH 5.6, vapor diffusion, sitting drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1843.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.833α = 90
b = 91.507β = 89.96
c = 73.232γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
12.2149.8393.30.1229.55.230618
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)
12.212.2981.10.4572.72634

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 REPLACEMENTTHROUGHOUTpdb entry 1OI22.2149.83305791561930.17380.17190.2099RANDOM30.6636
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]
-0.19-0.01-0.560.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.59
r_dihedral_angle_4_deg20.742
r_dihedral_angle_3_deg15.709
r_dihedral_angle_1_deg6.351
r_scangle_it2.839
r_scbond_it1.78
r_angle_refined_deg1.354
r_mcangle_it1.081
r_mcbond_it0.635
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.59
r_dihedral_angle_4_deg20.742
r_dihedral_angle_3_deg15.709
r_dihedral_angle_1_deg6.351
r_scangle_it2.839
r_scbond_it1.78
r_angle_refined_deg1.354
r_mcangle_it1.081
r_mcbond_it0.635
r_nbtor_refined0.301
r_symmetry_vdw_refined0.241
r_nbd_refined0.204
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.123
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5308
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing