X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VABPDB entry 2vab chains A and B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295K/NA PHOSPHATE, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0860.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.287α = 90
b = 88.342β = 90
c = 45.322γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2000-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.979SSRLBL9-1

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
11.73299.70.05614.93.760060-3
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)
11.71.7399.90.5911.43.72991

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 2vab chains A and B1.713254406289095.70.187610.186710.20431RANDOM21.198
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]
-0.741.34-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.04
r_scangle_it5.076
r_dihedral_angle_1_deg4.734
r_scbond_it3.054
r_angle_other_deg2.559
r_mcangle_it1.989
r_angle_refined_deg1.784
r_mcbond_it1.088
r_nbtor_other0.411
r_symmetry_hbond_refined0.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.04
r_scangle_it5.076
r_dihedral_angle_1_deg4.734
r_scbond_it3.054
r_angle_other_deg2.559
r_mcangle_it1.989
r_angle_refined_deg1.784
r_mcbond_it1.088
r_nbtor_other0.411
r_symmetry_hbond_refined0.229
r_nbd_refined0.222
r_nbd_other0.21
r_symmetry_hbond_other0.19
r_symmetry_vdw_other0.179
r_xyhbond_nbd_refined0.169
r_symmetry_vdw_refined0.155
r_chiral_restr0.153
r_xyhbond_nbd_other0.036
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.001
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3112
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing