X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KMEPDB ENTRY 1KME

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.4300.153.6M Sodium Phosphate (pH 3.4), 3.5% Triethyleneglycol, 180mM Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 300.15K
Crystal Properties
Matthews coefficientSolvent content
2.3748.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.16α = 90
b = 113.29β = 114.27
c = 56.19γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
1246.6796.60.0746.52.13539534192
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)
122.1195.10.551.72.15132

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1KME242.083539533257166798.290.159420.159420.158750.17183RANDOM28.373
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.693
r_dihedral_angle_4_deg15.504
r_dihedral_angle_3_deg14.49
r_dihedral_angle_1_deg4.877
r_angle_refined_deg1.879
r_angle_other_deg1.317
r_chiral_restr0.151
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.693
r_dihedral_angle_4_deg15.504
r_dihedral_angle_3_deg14.49
r_dihedral_angle_1_deg4.877
r_angle_refined_deg1.879
r_angle_other_deg1.317
r_chiral_restr0.151
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.007
r_gen_planes_other0.006
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3512
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms91

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling