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, 5 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.4148.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.946α = 90
b = 73.946β = 90
c = 128.584γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

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
12.225099.80.0980.0940.0278.314.110855
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.222.399.90.9810.2640.875141053

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 5CCY2.22501030852299.90.19380.19150.2411RANDOM44.192
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]
-0.66-0.33-0.662.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.406
r_dihedral_angle_4_deg16.968
r_dihedral_angle_3_deg14.256
r_dihedral_angle_1_deg5.742
r_mcangle_it2.726
r_mcbond_it1.653
r_mcbond_other1.651
r_angle_refined_deg1.483
r_angle_other_deg0.956
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.406
r_dihedral_angle_4_deg16.968
r_dihedral_angle_3_deg14.256
r_dihedral_angle_1_deg5.742
r_mcangle_it2.726
r_mcbond_it1.653
r_mcbond_other1.651
r_angle_refined_deg1.483
r_angle_other_deg0.956
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1458
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms23

Software

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