X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VJUPDB entry 1VJU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82771 ul Protein 11 mg/ml, 1 ul Crystallization buffer: 35% PEG 5000 MME, 200 mM Ammonium sulfate, 100 mM MES pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2445.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.083α = 86.28
b = 53.808β = 77.28
c = 65.828γ = 60.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2006-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97930APS23-ID-B

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
11.7546.9894.60.04915.23.35868218.03259
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)
11.751.81770.2291.84755

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 DIFFRACTIONTHROUGHOUTPDB entry 1VJU1.752058641295894.420.1660.1650.193RANDOM12.392
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]
-0.21-0.270.520.270.12-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.256
r_dihedral_angle_4_deg12.353
r_dihedral_angle_3_deg12.045
r_dihedral_angle_1_deg5.332
r_scangle_it1.441
r_angle_other_deg1.194
r_angle_refined_deg1.027
r_scbond_it0.96
r_mcangle_it0.65
r_mcbond_it0.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.256
r_dihedral_angle_4_deg12.353
r_dihedral_angle_3_deg12.045
r_dihedral_angle_1_deg5.332
r_scangle_it1.441
r_angle_other_deg1.194
r_angle_refined_deg1.027
r_scbond_it0.96
r_mcangle_it0.65
r_mcbond_it0.458
r_symmetry_vdw_other0.225
r_nbd_refined0.189
r_nbtor_refined0.184
r_nbd_other0.179
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.106
r_xyhbond_nbd_refined0.104
r_nbtor_other0.084
r_mcbond_other0.078
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4875
Nucleic Acid Atoms
Solvent Atoms532
Heterogen Atoms12

Software

Software
Software NamePurpose
TRUNCATEdata reduction
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
REFMACrefinement