X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GD9PDB ENTRY 1GD9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.429115%w/v PEG-3350, 0.4 micromoles per liter cesium chloride, 0.15M ammonium citrate, pH 7.4, modified microbatch, temperature 291K, pH 7.40
Crystal Properties
Matthews coefficientSolvent content
2.2845.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.804α = 90
b = 188.089β = 89.79
c = 72.583γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
12.335098.60.05369038
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)
12.332.4291.20.23

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 1GD92.3342.266899321001000.203350.2020.245THIN SHELLS27.17
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]
-0.072-0.0550.0460.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.766
r_dihedral_angle_4_deg17.82
r_dihedral_angle_3_deg14.23
r_dihedral_angle_1_deg5.541
r_scangle_it3.55
r_mcangle_it2.998
r_scbond_it2.416
r_mcbond_it1.829
r_angle_refined_deg1.471
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.766
r_dihedral_angle_4_deg17.82
r_dihedral_angle_3_deg14.23
r_dihedral_angle_1_deg5.541
r_scangle_it3.55
r_mcangle_it2.998
r_scbond_it2.416
r_mcbond_it1.829
r_angle_refined_deg1.471
r_nbtor_refined0.299
r_symmetry_vdw_refined0.216
r_nbd_refined0.192
r_xyhbond_nbd_refined0.124
r_chiral_restr0.1
r_symmetry_hbond_refined0.075
r_bond_refined_d0.013
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12162
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms60

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing