X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GOXPDB ENTRY 1GOX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829818-20%(w/v) PEG 8000, 50mM Tris buffer pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.754.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 191.096α = 90
b = 191.096β = 90
c = 194.497γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-12-10MSINGLE WAVELENGTH
21100IMAGE PLATEMAC Science, DIP6040
31100CCDMARRESEARCH
41100CCDADSC QUANTUM 4
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1
2SYNCHROTRONSPRING-8 BEAMLINE BL44XU1.0SPring-8BL44XU
3SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU
4SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
12.07461000.14222.7212.81085661085661119.47
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)
2.072.141000.436

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 1GOX2.1201110300610300654181000.161680.161680.15970.19904RANDOM19.443
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]
0.320.32-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.092
r_dihedral_angle_4_deg17.615
r_dihedral_angle_3_deg16.219
r_dihedral_angle_1_deg6.865
r_scangle_it4.002
r_scbond_it2.639
r_angle_refined_deg1.781
r_mcangle_it1.587
r_mcbond_it1.007
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.092
r_dihedral_angle_4_deg17.615
r_dihedral_angle_3_deg16.219
r_dihedral_angle_1_deg6.865
r_scangle_it4.002
r_scbond_it2.639
r_angle_refined_deg1.781
r_mcangle_it1.587
r_mcbond_it1.007
r_nbtor_refined0.312
r_nbd_refined0.22
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.141
r_chiral_restr0.132
r_bond_refined_d0.018
r_gen_planes_refined0.007
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_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11552
Nucleic Acid Atoms
Solvent Atoms1109
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing