X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ESBPDB ENTRY 2ESB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.40.1M SODIUM CITRATE PH 5.4, 1.1 M AMMONIUM PHOSPHATE MONOBASIC,0.1 M NDSB-256 CRYOPROTECTED WITH 20% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.4649.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.011α = 90
b = 85.011β = 90
c = 115.112γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMSC OSMIC MIRROR SYSTEM2008-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.885099.30.0822.87329502
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)
11.881.9593.40.651.94.6

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 2ESB1.885031259167099.250.177750.175480.22058RANDOM21.187
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_deg34.558
r_dihedral_angle_4_deg21.876
r_dihedral_angle_3_deg13.914
r_dihedral_angle_1_deg5.877
r_scangle_it2.943
r_scbond_it1.848
r_angle_refined_deg1.411
r_mcangle_it1.162
r_angle_other_deg1.031
r_mcbond_it0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.558
r_dihedral_angle_4_deg21.876
r_dihedral_angle_3_deg13.914
r_dihedral_angle_1_deg5.877
r_scangle_it2.943
r_scbond_it1.848
r_angle_refined_deg1.411
r_mcangle_it1.162
r_angle_other_deg1.031
r_mcbond_it0.66
r_mcbond_other0.192
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
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 Atoms2651
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing