X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UD9PDB entry 1UD9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529312.5% PEG 3350, 0.15 M NH4Cl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.773α = 90
b = 85.773β = 90
c = 264.21γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.100NSLSX25

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
11.95096.30.10232.223.37594775947
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)
11.91.9265.60.4912.25.8

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 1UD91.929.62758027427215301000.204930.204010.25055RANDOM38.571
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]
-0.38-0.380.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.681
r_dihedral_angle_4_deg16.618
r_dihedral_angle_3_deg15.974
r_dihedral_angle_1_deg7.262
r_scangle_it3.582
r_scbond_it2.505
r_angle_refined_deg1.641
r_mcangle_it1.393
r_mcbond_it1.157
r_angle_other_deg1.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.681
r_dihedral_angle_4_deg16.618
r_dihedral_angle_3_deg15.974
r_dihedral_angle_1_deg7.262
r_scangle_it3.582
r_scbond_it2.505
r_angle_refined_deg1.641
r_mcangle_it1.393
r_mcbond_it1.157
r_angle_other_deg1.096
r_mcbond_other0.35
r_symmetry_vdw_other0.264
r_symmetry_vdw_refined0.242
r_nbd_refined0.215
r_nbd_other0.188
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.175
r_symmetry_hbond_refined0.175
r_chiral_restr0.118
r_nbtor_other0.088
r_bond_refined_d0.016
r_xyhbond_nbd_other0.012
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7736
Nucleic Acid Atoms
Solvent Atoms535
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing