X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BYL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529680-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7855.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.43α = 90
b = 99.22β = 105.46
c = 93.51γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002013-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.390.13990.0850.9969.84.36920749.6
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)
12.32.3598.11.0931.54.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5BYL2.390.1365703350498.850.168930.166670.21071RANDOM58.064
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.53
r_dihedral_angle_3_deg13.923
r_dihedral_angle_4_deg12.608
r_long_range_B_refined8.225
r_long_range_B_other8.198
r_dihedral_angle_1_deg5.632
r_scangle_other5.108
r_mcangle_it3.397
r_mcangle_other3.396
r_scbond_it3.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.53
r_dihedral_angle_3_deg13.923
r_dihedral_angle_4_deg12.608
r_long_range_B_refined8.225
r_long_range_B_other8.198
r_dihedral_angle_1_deg5.632
r_scangle_other5.108
r_mcangle_it3.397
r_mcangle_other3.396
r_scbond_it3.337
r_scbond_other3.337
r_mcbond_it2.343
r_mcbond_other2.343
r_angle_refined_deg1.496
r_angle_other_deg1.19
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9569
Nucleic Acid Atoms
Solvent Atoms766
Heterogen Atoms271

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
REFMACphasing