X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D7Ypdb entry: 1D7Y including all side chains

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.72860.1 M Tris pH 8.5, 1.5 M (NH)4SO 2 and 12% (v/v) glycerol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties
Matthews coefficientSolvent content
2.7154.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.128α = 90
b = 77.128β = 90
c = 156.372γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1.0332NSLSX6A

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
11.819.86990.0769.244435211
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)
11.81.8696.40.38647.044216

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: 1D7Y including all side chains1.8204419844198222999.280.2050.2050.2030.243RANDOM28.002
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]
1.091.09-2.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.31
r_dihedral_angle_4_deg17.776
r_dihedral_angle_3_deg13.779
r_dihedral_angle_1_deg5.622
r_scangle_it3.389
r_scbond_it2.071
r_angle_refined_deg1.521
r_mcangle_it1.299
r_mcbond_it0.86
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.31
r_dihedral_angle_4_deg17.776
r_dihedral_angle_3_deg13.779
r_dihedral_angle_1_deg5.622
r_scangle_it3.389
r_scbond_it2.071
r_angle_refined_deg1.521
r_mcangle_it1.299
r_mcbond_it0.86
r_nbtor_refined0.297
r_symmetry_vdw_refined0.22
r_nbd_refined0.195
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.136
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2940
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms105

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
d*TREKdata reduction