3B1T

Crystal structure of human peptidylarginine deiminase 4 in complex with o-Cl-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
2.856.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.787α = 90
b = 60.853β = 123.99
c = 114.302γ = 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
12.55027393

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 1WDA2.5202734613671000.21380.21110.2629RANDOM75.845
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]
-2.54-1.862.18-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.697
r_dihedral_angle_3_deg20.079
r_dihedral_angle_4_deg18.219
r_dihedral_angle_1_deg7.455
r_angle_other_deg3.379
r_angle_refined_deg1.484
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.697
r_dihedral_angle_3_deg20.079
r_dihedral_angle_4_deg18.219
r_dihedral_angle_1_deg7.455
r_angle_other_deg3.379
r_angle_refined_deg1.484
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4912
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement