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
2.8556.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.18α = 90
b = 100.36β = 105.3
c = 93.94γ = 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
12.590.611000.1140.99110.64.75597452.1
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)
12.52.571001.04724.7

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 SYNTHESISTHROUGHOUT5BYL2.590.6153133280499.940.171080.168750.2145RANDOM69.533
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]
-0.04-0.01-0.030.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_dihedral_angle_3_deg14.723
r_dihedral_angle_4_deg11.464
r_long_range_B_other8.27
r_long_range_B_refined8.265
r_dihedral_angle_1_deg5.487
r_scangle_other5.245
r_mcangle_other3.819
r_mcangle_it3.818
r_scbond_it3.289
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_dihedral_angle_3_deg14.723
r_dihedral_angle_4_deg11.464
r_long_range_B_other8.27
r_long_range_B_refined8.265
r_dihedral_angle_1_deg5.487
r_scangle_other5.245
r_mcangle_other3.819
r_mcangle_it3.818
r_scbond_it3.289
r_scbond_other3.288
r_mcbond_it2.47
r_mcbond_other2.468
r_angle_refined_deg1.487
r_angle_other_deg1.406
r_chiral_restr0.096
r_bond_refined_d0.013
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 Atoms9669
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms310

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
REFMACphasing