X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CCYPDB entry 5CCY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52910.2 M magnesium chloride, 2 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.2946.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.683α = 90
b = 73.683β = 90
c = 128.053γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2015-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.155099.50.0760.0780.0211.615.511735
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2398.70.7320.7610.2060.878131131

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 5CCY2.15501106063899.370.18860.18510.2514RANDOM47.2
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]
-0.87-0.43-0.872.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.163
r_dihedral_angle_4_deg19.592
r_dihedral_angle_3_deg15.757
r_dihedral_angle_1_deg7.018
r_mcangle_it3.955
r_mcbond_other2.714
r_mcbond_it2.713
r_angle_refined_deg2.303
r_angle_other_deg1.177
r_chiral_restr0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.163
r_dihedral_angle_4_deg19.592
r_dihedral_angle_3_deg15.757
r_dihedral_angle_1_deg7.018
r_mcangle_it3.955
r_mcbond_other2.714
r_mcbond_it2.713
r_angle_refined_deg2.303
r_angle_other_deg1.177
r_chiral_restr0.131
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1441
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms2

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing