X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V9KPDB ENTRY 1V9K (molecule A)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8277Bicine, sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2645.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.307α = 90
b = 97.307β = 90
c = 86.237γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATEMARRESEARCHmirrors1998-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
12.2301000.06738.4142438124381
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)
12.22.281000.4416.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1V9K (molecule A)2.2302433623094124299.940.188050.184620.25372RANDOM33.656
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]
0.080.040.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.194
r_dihedral_angle_4_deg20.938
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg7.376
r_scangle_it4.888
r_scbond_it3.176
r_mcangle_it2.061
r_angle_refined_deg1.906
r_mcbond_it1.311
r_symmetry_hbond_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.194
r_dihedral_angle_4_deg20.938
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg7.376
r_scangle_it4.888
r_scbond_it3.176
r_mcangle_it2.061
r_angle_refined_deg1.906
r_mcbond_it1.311
r_symmetry_hbond_refined0.311
r_nbtor_refined0.301
r_nbd_refined0.209
r_symmetry_vdw_refined0.209
r_xyhbond_nbd_refined0.167
r_chiral_restr0.127
r_bond_refined_d0.022
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3608
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing