X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293NaOAc, PEG4000, Glycerol, Tris
Crystal Properties
Matthews coefficientSolvent content
2.2244.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.71α = 90.05
b = 49.79β = 93.48
c = 71.49γ = 101.91
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9762ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9471.35190.90.1090.1320.0756.72.84506745067
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.942.0485.10.1680.1680.2060.1173.92.76152

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 REPLACEMENTTHROUGHOUT5HND1.9471.3542796227190.950.19840.19640.2369RANDOM15.915
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]
1.780.06-0.26-0.68-0.1-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.007
r_dihedral_angle_4_deg19.106
r_dihedral_angle_3_deg13.726
r_dihedral_angle_1_deg6.387
r_mcangle_it1.157
r_angle_refined_deg0.873
r_mcbond_it0.732
r_mcbond_other0.731
r_angle_other_deg0.535
r_chiral_restr0.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.007
r_dihedral_angle_4_deg19.106
r_dihedral_angle_3_deg13.726
r_dihedral_angle_1_deg6.387
r_mcangle_it1.157
r_angle_refined_deg0.873
r_mcbond_it0.732
r_mcbond_other0.731
r_angle_other_deg0.535
r_chiral_restr0.048
r_gen_planes_refined0.006
r_bond_other_d0.005
r_bond_refined_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5466
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
iMOSFLMdata reduction