X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B4GPDB entry 2B4G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION52982.545M Sodium chloride, 0.1M Citric acid, 5mM Orotic acid pH 5.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8256.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.869α = 90
b = 83.869β = 90
c = 188.725γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2007-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97950SSRLBL9-2

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
11.8501000.0989.15.2137519
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)
11.81.8699.90.5154.613796

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 2B4G1.833.88137496690299.960.1680.1660.196RANDOM18.249
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]
0.270.130.27-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.66
r_dihedral_angle_4_deg14.246
r_dihedral_angle_3_deg12.41
r_dihedral_angle_1_deg6.16
r_scangle_it3.652
r_scbond_it2.258
r_angle_refined_deg1.401
r_mcangle_it1.371
r_angle_other_deg0.949
r_mcbond_it0.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.66
r_dihedral_angle_4_deg14.246
r_dihedral_angle_3_deg12.41
r_dihedral_angle_1_deg6.16
r_scangle_it3.652
r_scbond_it2.258
r_angle_refined_deg1.401
r_mcangle_it1.371
r_angle_other_deg0.949
r_mcbond_it0.751
r_mcbond_other0.192
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9532
Nucleic Acid Atoms
Solvent Atoms752
Heterogen Atoms212

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection