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, PEG 3350, pH9.6, NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.26α = 90
b = 58.676β = 90
c = 106.846γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-DAPS14-BM-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
125099.40.0996.72005822

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: 1yc51.995021890017895101599.750.19770.195590.23683RANDOM24.435
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]
2.18-0.73-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.361
r_dihedral_angle_4_deg24.716
r_dihedral_angle_3_deg14.269
r_dihedral_angle_1_deg6.096
r_scangle_it4.365
r_scbond_it2.84
r_angle_refined_deg1.947
r_mcangle_it1.855
r_mcbond_it1.12
r_nbtor_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.361
r_dihedral_angle_4_deg24.716
r_dihedral_angle_3_deg14.269
r_dihedral_angle_1_deg6.096
r_scangle_it4.365
r_scbond_it2.84
r_angle_refined_deg1.947
r_mcangle_it1.855
r_mcbond_it1.12
r_nbtor_refined0.332
r_symmetry_hbond_refined0.295
r_nbd_refined0.266
r_symmetry_vdw_refined0.265
r_xyhbond_nbd_refined0.17
r_chiral_restr0.109
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1908
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms45

Software

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