X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JD0PDB ENTRY 1JD0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52910.1M ammonium citrate with pH 5.0 and 16% of PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.709α = 81.78
b = 67.261β = 84.01
c = 80.689γ = 86.48
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMirror Bent, vertically focussing2011-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

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
11.4527.16497.10.0390.03914.1416617911.3
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)
11.451.5395.60.2190.2193.4423905

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 1JD01.4526.51661791661771645597.080.1540.1540.150.188RANDOM12.981
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]
-0.330.050.02-0.10.490.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.671
r_dihedral_angle_4_deg18.181
r_dihedral_angle_3_deg13.132
r_dihedral_angle_1_deg7.373
r_scangle_it4.448
r_scbond_it3.129
r_angle_refined_deg2.462
r_mcangle_it2.214
r_mcbond_it1.432
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.671
r_dihedral_angle_4_deg18.181
r_dihedral_angle_3_deg13.132
r_dihedral_angle_1_deg7.373
r_scangle_it4.448
r_scbond_it3.129
r_angle_refined_deg2.462
r_mcangle_it2.214
r_mcbond_it1.432
r_nbtor_refined0.311
r_symmetry_vdw_refined0.26
r_nbd_refined0.228
r_chiral_restr0.2
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.167
r_metal_ion_refined0.037
r_bond_refined_d0.031
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8392
Nucleic Acid Atoms
Solvent Atoms1504
Heterogen Atoms165

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
DNAdata collection
MOLREPphasing