X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JM6PDK2 PDB entry 1JM6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6293soudium citrate, sodium potassium phosphate, sodium chrolide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.773.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.904α = 90
b = 120.904β = 90
c = 240.085γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3102003-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97APS19-ID

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
12.625098.40.059307.53153831043-3
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)
12.622.7197.20.5422.15.12970

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDK2 PDB entry 1JM62.63503104329477156698.340.204950.204950.203580.2302RANDOM66.251
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]
-0.79-0.39-0.791.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.041
r_dihedral_angle_3_deg20.209
r_dihedral_angle_4_deg17.618
r_dihedral_angle_1_deg6.37
r_scangle_it3.572
r_scbond_it2.201
r_angle_refined_deg1.731
r_mcangle_it1.297
r_mcbond_it0.679
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.041
r_dihedral_angle_3_deg20.209
r_dihedral_angle_4_deg17.618
r_dihedral_angle_1_deg6.37
r_scangle_it3.572
r_scbond_it2.201
r_angle_refined_deg1.731
r_mcangle_it1.297
r_mcbond_it0.679
r_nbtor_refined0.322
r_nbd_refined0.25
r_symmetry_vdw_refined0.21
r_metal_ion_refined0.182
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.134
r_chiral_restr0.111
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3836
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing