5OCX

Crystal structure of ACPA E4 in complex with CII-C-13-CIT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4M1Q4M1Q,3LMJ
experimental modelPDB 3LMJ4M1Q,3LMJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% (w/v) PEG3350, 0.2 M ammonium citrate dibasic
Crystal Properties
Matthews coefficientSolvent content
1.8232.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.716α = 90
b = 99.602β = 101.88
c = 51.877γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7545.2397.30.0830.0760.9947.53.13766015.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.78900.5840.5390.6061.32.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4M1Q,3LMJ1.7545.2335680194897.130.178120.176230.21231RANDOM23.114
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]
0.191.04-2.031.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.371
r_dihedral_angle_4_deg22.595
r_dihedral_angle_3_deg11.687
r_dihedral_angle_1_deg6.606
r_long_range_B_refined4.627
r_long_range_B_other4.627
r_scangle_other2.443
r_mcangle_other2.195
r_mcangle_it2.193
r_angle_other_deg1.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.371
r_dihedral_angle_4_deg22.595
r_dihedral_angle_3_deg11.687
r_dihedral_angle_1_deg6.606
r_long_range_B_refined4.627
r_long_range_B_other4.627
r_scangle_other2.443
r_mcangle_other2.195
r_mcangle_it2.193
r_angle_other_deg1.581
r_scbond_it1.532
r_scbond_other1.531
r_angle_refined_deg1.428
r_mcbond_it1.337
r_mcbond_other1.334
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3356
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing