X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YCRPDB ENTRY 1YCR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.530025% PEG3350, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.1542.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.73α = 90
b = 58.87β = 92
c = 96.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2008-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

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
11.940960.05532474312922
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)
1.92860.1957

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1YCR1.919.78230432162698.820.199780.196570.2571RANDOM17.327
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]
0.99-0.490.04-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.988
r_dihedral_angle_4_deg18.242
r_dihedral_angle_3_deg14.745
r_dihedral_angle_1_deg10.365
r_scangle_it2.722
r_scbond_it1.861
r_angle_refined_deg1.354
r_mcangle_it1.261
r_angle_other_deg1.089
r_mcbond_it0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.988
r_dihedral_angle_4_deg18.242
r_dihedral_angle_3_deg14.745
r_dihedral_angle_1_deg10.365
r_scangle_it2.722
r_scbond_it1.861
r_angle_refined_deg1.354
r_mcangle_it1.261
r_angle_other_deg1.089
r_mcbond_it0.85
r_symmetry_vdw_refined0.351
r_symmetry_vdw_other0.269
r_nbd_refined0.207
r_nbd_other0.184
r_symmetry_hbond_refined0.183
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.163
r_mcbond_other0.161
r_chiral_restr0.127
r_nbtor_other0.085
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3151
Nucleic Acid Atoms
Solvent Atoms429
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing