X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NOMPDB ENTRY 3NOM

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.9235.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.79α = 90
b = 46.06β = 112.97
c = 81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.652097.90.05915.5652886-323.626
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7594.30.5460.6522.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3NOM1.6519.8752874264698.040.19690.19480.2361RANDOM19.2743
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]
0.020.54-0.140.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.629
r_dihedral_angle_4_deg18.295
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg7.047
r_scangle_it4.673
r_scbond_it3.065
r_angle_refined_deg2.072
r_mcangle_it2.007
r_mcbond_it1.256
r_chiral_restr0.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.629
r_dihedral_angle_4_deg18.295
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg7.047
r_scangle_it4.673
r_scbond_it3.065
r_angle_refined_deg2.072
r_mcangle_it2.007
r_mcbond_it1.256
r_chiral_restr0.227
r_bond_refined_d0.024
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3636
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms60

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction