X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QJD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82770.1M TrisHCl, 80mM NaCl, 10mM Na fumarate, 15% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6152.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.961α = 90
b = 92.879β = 91.17
c = 79.486γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2001-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.87EMBL/DESY, HAMBURGBW7B

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
11.72098.40.06718.7734087217818.3
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)
1.71.7694.60.1296.96862

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 REPLACEMENTTHROUGHOUT1QJD1.72068525362998.210.157680.156460.18034RANDOM18.322
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]
0.71-0.160.4-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.491
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg11.902
r_dihedral_angle_1_deg5.579
r_scangle_it2.742
r_scbond_it1.772
r_angle_refined_deg1.314
r_mcangle_it1.009
r_mcbond_it0.561
r_nbtor_refined0.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.491
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg11.902
r_dihedral_angle_1_deg5.579
r_scangle_it2.742
r_scbond_it1.772
r_angle_refined_deg1.314
r_mcangle_it1.009
r_mcbond_it0.561
r_nbtor_refined0.283
r_nbd_refined0.226
r_symmetry_vdw_refined0.118
r_symmetry_hbond_refined0.116
r_xyhbond_nbd_refined0.114
r_chiral_restr0.111
r_metal_ion_refined0.035
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4176
Nucleic Acid Atoms
Solvent Atoms1084
Heterogen Atoms234

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing