9GT0 | pdb_00009gt0

DTPAA CHIP EXPERIMENT, ID29, X,Y SPACING 100,100


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I4C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE293PEG 6K, HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.6α = 90
b = 68.8β = 105.8
c = 75.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELPSI JUNGFRAU 4M2024-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.073ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Split (All)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
11.67401000.122770084225
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.711.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6737.6679872432599.940.147480.14610.16050.171570.184RANDOM24.068
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]
0.26-0.24-0.540.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.63
r_dihedral_angle_4_deg17.334
r_dihedral_angle_3_deg13.556
r_long_range_B_refined9.319
r_long_range_B_other8.97
r_dihedral_angle_1_deg6.614
r_scangle_other5.013
r_scbond_other3.196
r_scbond_it3.195
r_mcangle_it2.647
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.63
r_dihedral_angle_4_deg17.334
r_dihedral_angle_3_deg13.556
r_long_range_B_refined9.319
r_long_range_B_other8.97
r_dihedral_angle_1_deg6.614
r_scangle_other5.013
r_scbond_other3.196
r_scbond_it3.195
r_mcangle_it2.647
r_mcangle_other2.633
r_mcbond_it1.917
r_mcbond_other1.89
r_angle_refined_deg1.682
r_angle_other_deg1.423
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5539
Nucleic Acid Atoms
Solvent Atoms598
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata scaling
CrystFELdata reduction
PHASERphasing