X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QIVPDB ENTRY 1QIV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295PEG 6000, sodium acetate, calcium chrolide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.141.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.229α = 90
b = 40.229β = 90
c = 343.468γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90IMAGE PLATERIGAKU RAXIS V2000-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45PX1.02SPring-8BL45PX

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
1220095.90.07914.27.6124671195631.55
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)
22.07980.271149

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1QIV2201117221133656996.70.225130.223080.26686RANDOM38.144
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]
0.750.370.75-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.455
r_scangle_it5.497
r_scbond_it3.384
r_dihedral_angle_1_deg3.101
r_mcangle_it2.31
r_angle_refined_deg1.653
r_mcbond_it1.299
r_angle_other_deg0.87
r_nbd_refined0.262
r_nbd_other0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.455
r_scangle_it5.497
r_scbond_it3.384
r_dihedral_angle_1_deg3.101
r_mcangle_it2.31
r_angle_refined_deg1.653
r_mcbond_it1.299
r_angle_other_deg0.87
r_nbd_refined0.262
r_nbd_other0.228
r_symmetry_vdw_other0.216
r_xyhbond_nbd_refined0.169
r_metal_ion_refined0.154
r_symmetry_hbond_refined0.138
r_symmetry_vdw_refined0.13
r_chiral_restr0.1
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1225
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement