4OGY

Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ANYPDB ENTRY 2ANY AND 3IDX
experimental modelPDB 3IDXPDB ENTRY 2ANY AND 3IDX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST INDEX screen condition D10, 20% PEG 5000 MME, 0.1 M BisTris pH 6.5 supplemented with 20% ethylene glycol as cryo-protectant, unique puck ID qjo1-15, crystal tracking ID 242121d10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.12α = 90
b = 113.76β = 94.7
c = 89.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+VARIMAX2013-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.15099.80.07622.67.39508494897-328.24
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)
12.12.1498.80.3465.86.1

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 2ANY AND 3IDX2.140.5994873475799.820.1850.1830.221RANDOM26.51
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]
0.31-0.07-0.15-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.178
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg13.144
r_dihedral_angle_1_deg6.553
r_mcangle_it1.441
r_angle_refined_deg1.361
r_angle_other_deg0.954
r_mcbond_it0.807
r_mcbond_other0.807
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.178
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg13.144
r_dihedral_angle_1_deg6.553
r_mcangle_it1.441
r_angle_refined_deg1.361
r_angle_other_deg0.954
r_mcbond_it0.807
r_mcbond_other0.807
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.004
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_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9991
Nucleic Acid Atoms
Solvent Atoms1020
Heterogen Atoms12

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction