1WDA

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293PEGMME2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.133α = 90
b = 60.045β = 124.23
c = 115.406γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102003-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.9000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.342.5297.90.0510.33671836718
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3893.50.2172.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.342.523264632646366197.90.215070.21480.210450.25211RANDOM44.287
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]
-7.64-5.127.1-5.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.11
r_scangle_it2.777
r_scbond_it1.681
r_angle_refined_deg1.593
r_mcangle_it1.292
r_angle_other_deg1.013
r_mcbond_it0.708
r_symmetry_hbond_refined0.335
r_nbd_other0.236
r_nbd_refined0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.11
r_scangle_it2.777
r_scbond_it1.681
r_angle_refined_deg1.593
r_mcangle_it1.292
r_angle_other_deg1.013
r_mcbond_it0.708
r_symmetry_hbond_refined0.335
r_nbd_other0.236
r_nbd_refined0.209
r_symmetry_vdw_other0.209
r_xyhbond_nbd_refined0.189
r_chiral_restr0.152
r_metal_ion_refined0.118
r_symmetry_vdw_refined0.096
r_nbtor_other0.089
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4946
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing