5Q87

PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 216)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629830% PEG 1000, 0.1M MIB buffer
Crystal Properties
Matthews coefficientSolvent content
2.1943.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.986α = 90
b = 56.906β = 90
c = 115.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELDECTRIS PILATUS 6M2017-04-12SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.3456.91000.050.0550.022113.1677504
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.341.3799.71.2571.4140.6330.514.85656

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5aho1.3456.973274375499.370.20540.20420.2295RANDOM23.539
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]
-0.020.73-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.56
r_dihedral_angle_4_deg17.529
r_dihedral_angle_3_deg12.541
r_dihedral_angle_1_deg6.685
r_mcangle_it3.76
r_mcbond_it2.541
r_mcbond_other2.536
r_angle_refined_deg2.226
r_angle_other_deg1.125
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.56
r_dihedral_angle_4_deg17.529
r_dihedral_angle_3_deg12.541
r_dihedral_angle_1_deg6.685
r_mcangle_it3.76
r_mcbond_it2.541
r_mcbond_other2.536
r_angle_refined_deg2.226
r_angle_other_deg1.125
r_chiral_restr0.133
r_bond_refined_d0.026
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2692
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing