X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YC5PDB Entry: 1yc5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.6293CHES, PEG3350, NAD, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.821α = 90
b = 59.331β = 90
c = 106.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.36CCDADSC QUANTUM 3152005-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.0APS24-ID-C

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
125098.72004812

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: 1yc525022000018976102498.350.194060.192260.22823RANDOM30.415
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]
0.990.36-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.348
r_dihedral_angle_4_deg28.224
r_dihedral_angle_3_deg15.097
r_dihedral_angle_1_deg7.858
r_scangle_it4.953
r_scbond_it3.067
r_mcangle_it2.04
r_angle_refined_deg1.78
r_mcbond_it1.249
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.348
r_dihedral_angle_4_deg28.224
r_dihedral_angle_3_deg15.097
r_dihedral_angle_1_deg7.858
r_scangle_it4.953
r_scbond_it3.067
r_mcangle_it2.04
r_angle_refined_deg1.78
r_mcbond_it1.249
r_nbtor_refined0.306
r_nbd_refined0.239
r_symmetry_vdw_refined0.231
r_symmetry_hbond_refined0.192
r_xyhbond_nbd_refined0.152
r_chiral_restr0.144
r_bond_refined_d0.017
r_gen_planes_refined0.007
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 Atoms1933
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
CNSphasing