X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VA4PDB ENTRY 1VA4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52951.7 M ammonium phosphate, 0.1 M Na,K phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1442.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.586α = 90
b = 145.586β = 90
c = 128.2γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315double crystal monochrometer2005-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.1NSLSX29A

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
11.948.196.50.05610.52.6223104223104223.2
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)
1.91.9793.50.31332.5422477

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 1VA41.948.12193501162596.420.191130.190010.2124RANDOM23.529
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]
-1.03-0.51-1.031.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.889
r_dihedral_angle_4_deg16.819
r_dihedral_angle_3_deg11.884
r_dihedral_angle_1_deg4.684
r_scangle_it1.881
r_scbond_it1.084
r_angle_refined_deg0.93
r_mcangle_it0.7
r_mcbond_it0.361
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.889
r_dihedral_angle_4_deg16.819
r_dihedral_angle_3_deg11.884
r_dihedral_angle_1_deg4.684
r_scangle_it1.881
r_scbond_it1.084
r_angle_refined_deg0.93
r_mcangle_it0.7
r_mcbond_it0.361
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12888
Nucleic Acid Atoms
Solvent Atoms1057
Heterogen Atoms250

Software

Software
Software NamePurpose
CBASSdata collection
Omodel building
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling