3B1U

Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WDAPDB ENTRY 1WDA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8156.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.422α = 90
b = 60.468β = 124.43
c = 115.506γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702009-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.15044771

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1WDA2.1204246422541000.220860.219280.2502RANDOM79.135
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]
-3.52-2.672.83-2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.774
r_dihedral_angle_3_deg13.767
r_dihedral_angle_4_deg13.693
r_dihedral_angle_1_deg5.551
r_angle_other_deg3.025
r_angle_refined_deg0.887
r_scangle_it0.794
r_mcangle_it0.485
r_scbond_it0.467
r_mcbond_it0.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.774
r_dihedral_angle_3_deg13.767
r_dihedral_angle_4_deg13.693
r_dihedral_angle_1_deg5.551
r_angle_other_deg3.025
r_angle_refined_deg0.887
r_scangle_it0.794
r_mcangle_it0.485
r_scbond_it0.467
r_mcbond_it0.261
r_chiral_restr0.055
r_mcbond_other0.028
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_gen_planes_other0.002
r_bond_other_d
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4947
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement