X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EBKpdb entry 3EBK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M HEPES, 1.5 M sodium citrate, 3% acetone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.856.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.354α = 90
b = 60.354β = 90
c = 125.409γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-01-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C0.9797, 0.9799, 0.9600NSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.755099.90.0640.06443.2154538645386-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.811000.50.54.7514.9

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 entry 3EBK1.7534.392294822948122999.930.18710.185690.21346RANDOM37.01
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]
0.150.15-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.188
r_dihedral_angle_4_deg19.627
r_dihedral_angle_3_deg13.636
r_dihedral_angle_1_deg6.758
r_angle_other_deg3.853
r_angle_refined_deg2.233
r_chiral_restr0.129
r_gen_planes_other0.031
r_bond_refined_d0.024
r_gen_planes_refined0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.188
r_dihedral_angle_4_deg19.627
r_dihedral_angle_3_deg13.636
r_dihedral_angle_1_deg6.758
r_angle_other_deg3.853
r_angle_refined_deg2.233
r_chiral_restr0.129
r_gen_planes_other0.031
r_bond_refined_d0.024
r_gen_planes_refined0.014
r_bond_other_d
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1370
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms35

Software

Software
Software NamePurpose
CBASSdata collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling