X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N40 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7278PEG 3350 and 0.2M NaSCN, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.4549.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.627α = 90
b = 129.758β = 90
c = 323.757γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.93ESRFID14-3

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
11.62093.20.0828.3314231314231

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1N401.6203142313142311669293.20.166930.166930.164650.21022RANDOM23.496
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]
0.28-0.14-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.121
r_dihedral_angle_4_deg16.593
r_dihedral_angle_3_deg13.325
r_sphericity_free7.768
r_dihedral_angle_1_deg5.36
r_scangle_it3.963
r_sphericity_bonded3.06
r_scbond_it2.935
r_rigid_bond_restr1.922
r_mcangle_it1.913
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.121
r_dihedral_angle_4_deg16.593
r_dihedral_angle_3_deg13.325
r_sphericity_free7.768
r_dihedral_angle_1_deg5.36
r_scangle_it3.963
r_sphericity_bonded3.06
r_scbond_it2.935
r_rigid_bond_restr1.922
r_mcangle_it1.913
r_angle_refined_deg1.534
r_mcbond_it1.425
r_angle_other_deg0.913
r_mcbond_other0.66
r_symmetry_vdw_other0.306
r_nbd_refined0.223
r_symmetry_hbond_refined0.215
r_nbd_other0.19
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.158
r_xyhbond_nbd_other0.152
r_symmetry_vdw_refined0.127
r_chiral_restr0.092
r_nbtor_other0.085
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17799
Nucleic Acid Atoms
Solvent Atoms2634
Heterogen Atoms288

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing