X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YMMPDB ENTRY 1YMM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.30.2 M LISO4, 0.8 M K2HPO4, 1.2 M NAH2PO4, 0.1 M CAPS PH 10.5, 8 % 1,1,1,3,3, 3-HEXAFLUORO-2-PROPANOL
Crystal Properties
Matthews coefficientSolvent content
3.4764.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.706α = 90
b = 130.271β = 90
c = 180.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
13.15301000.2310.316.9453611
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)
13.153.2610012.116.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1YMM3105.4149485265999.470.249090.246970.28778RANDOM64.111
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]
-1.07-3.294.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.29
r_dihedral_angle_3_deg22.277
r_dihedral_angle_4_deg19.879
r_dihedral_angle_1_deg9.407
r_scangle_it3.088
r_scbond_it1.944
r_mcangle_it1.672
r_mcbond_it1.019
r_angle_refined_deg1
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.29
r_dihedral_angle_3_deg22.277
r_dihedral_angle_4_deg19.879
r_dihedral_angle_1_deg9.407
r_scangle_it3.088
r_scbond_it1.944
r_mcangle_it1.672
r_mcbond_it1.019
r_angle_refined_deg1
r_nbtor_refined0.302
r_nbd_refined0.191
r_symmetry_vdw_refined0.159
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.115
r_chiral_restr0.07
r_bond_refined_d0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13103
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing