5Q1K

PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000074a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629830% PEG1000, 0.1 M MIB buffer
Crystal Properties
Matthews coefficientSolvent content
2.244.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.05α = 90
b = 57.22β = 90
c = 115.26γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELDECTRIS PILATUS 6M2016-09-29MSINGLE 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
11.4252.0599.30.0650.0710.0280.99913.76.565269
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)
11.421.4698.41.331.4670.6080.5155.74738

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 SYNTHESISTHROUGHOUT5aho1.4252.0562054315099.070.15480.15310.187RANDOM26.596
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]
0.160.93-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.965
r_sphericity_free30.535
r_sphericity_bonded12.675
r_dihedral_angle_3_deg11.335
r_dihedral_angle_4_deg9.627
r_dihedral_angle_1_deg6.271
r_mcangle_it2.733
r_mcbond_it2.078
r_mcbond_other2.063
r_angle_refined_deg1.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.965
r_sphericity_free30.535
r_sphericity_bonded12.675
r_dihedral_angle_3_deg11.335
r_dihedral_angle_4_deg9.627
r_dihedral_angle_1_deg6.271
r_mcangle_it2.733
r_mcbond_it2.078
r_mcbond_other2.063
r_angle_refined_deg1.364
r_rigid_bond_restr1.253
r_angle_other_deg0.953
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2696
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing