X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZSD1ZSD, 2NW2
experimental modelPDB 2NW21ZSD, 2NW2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.42770.1M Na Cacodylate (pH6.4), 0.2M CaCl2, 16% PEG 3350, 3% 1,6Hexanediol, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4549.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.479α = 90
b = 118.067β = 96.04
c = 131.465γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002005-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.787783

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 REPLACEMENTTHROUGHOUT1ZSD, 2NW22.73087783459893.520.271690.268760.32702RANDOM44.267
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]
0.760.171.64-2.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.788
r_dihedral_angle_3_deg16.581
r_dihedral_angle_4_deg15.895
r_dihedral_angle_1_deg5.246
r_scangle_it2.731
r_scbond_it1.806
r_mcangle_it1.5
r_angle_refined_deg0.959
r_mcbond_it0.829
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.788
r_dihedral_angle_3_deg16.581
r_dihedral_angle_4_deg15.895
r_dihedral_angle_1_deg5.246
r_scangle_it2.731
r_scbond_it1.806
r_mcangle_it1.5
r_angle_refined_deg0.959
r_mcbond_it0.829
r_nbtor_refined0.299
r_symmetry_vdw_refined0.204
r_nbd_refined0.188
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.137
r_chiral_restr0.066
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms26287
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction