X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ERTPDB ENTRY 1ERT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.629830% PEG 4000, 200 mM ammonium acetate, 100 mM sodium citrate, 5 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9235.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.233α = 90
b = 46.207β = 93.25
c = 52.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDRH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR2009-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
11.13096.90.047404.96964413.3
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)
1.11.1491.30.3983.24.1

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 1ERT1.117.8369636353696.90.1450.1440.172RANDOM14.96
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]
0.24-0.03-0.1-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.545
r_dihedral_angle_3_deg13.645
r_scangle_it6.128
r_dihedral_angle_1_deg5.935
r_scbond_it4.099
r_mcangle_it2.757
r_mcbond_it1.849
r_angle_refined_deg1.698
r_rigid_bond_restr1.632
r_angle_other_deg0.936
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.545
r_dihedral_angle_3_deg13.645
r_scangle_it6.128
r_dihedral_angle_1_deg5.935
r_scbond_it4.099
r_mcangle_it2.757
r_mcbond_it1.849
r_angle_refined_deg1.698
r_rigid_bond_restr1.632
r_angle_other_deg0.936
r_mcbond_other0.626
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1642
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
HKL-2000data reduction