X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IM4PDB entries 1IM4 and 1K1Q
experimental modelPDB 1K1QPDB entries 1IM4 and 1K1Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG-3350, calcium acetate, glycerol, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5651.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.416α = 90
b = 119.416β = 90
c = 68.274γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-10-21SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9795NSLSX25

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
12.62089.30.04835.44.614027-1
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)
12.62.6481.40.3143.42.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 entries 1IM4 and 1K1Q2.619.9138041312567988.150.217110.213870.27904RANDOM52.826
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]
3.073.07-6.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.56
r_dihedral_angle_3_deg18.777
r_dihedral_angle_4_deg15.758
r_dihedral_angle_1_deg5.532
r_scangle_it1.466
r_angle_refined_deg1.246
r_scbond_it0.859
r_mcangle_it0.698
r_mcbond_it0.398
r_metal_ion_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.56
r_dihedral_angle_3_deg18.777
r_dihedral_angle_4_deg15.758
r_dihedral_angle_1_deg5.532
r_scangle_it1.466
r_angle_refined_deg1.246
r_scbond_it0.859
r_mcangle_it0.698
r_mcbond_it0.398
r_metal_ion_refined0.311
r_nbtor_refined0.306
r_nbd_refined0.207
r_symmetry_hbond_refined0.203
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.136
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2704
Nucleic Acid Atoms462
Solvent Atoms110
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling