X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MJCPDB ENTRY 3MJC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.752933.1 M ammonium sulfate, 200 mM NaCl, 100 mM sodium cacodylate, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.654α = 72.99
b = 63.762β = 67.21
c = 71.744γ = 89.79
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.3662.7693.30.04828.22191224214
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)
1.361.3890.60.2643.71.9

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 3MJC1.3662.76191224965893.30.2030.2020.225RANDOM15.86
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]
0.20.14-0.14-0.21-0.350.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.175
r_dihedral_angle_4_deg20.409
r_dihedral_angle_3_deg14.684
r_dihedral_angle_1_deg6.253
r_scangle_it5.075
r_scbond_it3.483
r_angle_refined_deg2.725
r_mcangle_it2.406
r_mcbond_it1.564
r_chiral_restr0.281
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.175
r_dihedral_angle_4_deg20.409
r_dihedral_angle_3_deg14.684
r_dihedral_angle_1_deg6.253
r_scangle_it5.075
r_scbond_it3.483
r_angle_refined_deg2.725
r_mcangle_it2.406
r_mcbond_it1.564
r_chiral_restr0.281
r_bond_refined_d0.033
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6828
Nucleic Acid Atoms
Solvent Atoms474
Heterogen Atoms102

Software

Software
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling