5Q3F

PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 43)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629830% PEG 1000, 0.1M MIB buffer
Crystal Properties
Matthews coefficientSolvent content
2.244.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.06α = 90
b = 57.12β = 90
c = 115.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELDECTRIS PILATUS 6M2016-09-29SINGLE 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
11.3957.1299.90.0880.0960.0390.99710.75.869979
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)
11.391.4399.91.0131.150.5340.4744.55107

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 SYNTHESISTHROUGHOUT5aho1.3957.1266506339599.860.18860.18730.214RANDOM24.74
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]
0.090.82-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.566
r_dihedral_angle_4_deg18.023
r_dihedral_angle_3_deg12.648
r_dihedral_angle_1_deg6.704
r_mcangle_it4.052
r_mcbond_it2.713
r_mcbond_other2.706
r_angle_refined_deg2.254
r_angle_other_deg1.145
r_chiral_restr0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.566
r_dihedral_angle_4_deg18.023
r_dihedral_angle_3_deg12.648
r_dihedral_angle_1_deg6.704
r_mcangle_it4.052
r_mcbond_it2.713
r_mcbond_other2.706
r_angle_refined_deg2.254
r_angle_other_deg1.145
r_chiral_restr0.141
r_bond_refined_d0.027
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