5PAR

Crystal Structure of Factor VIIa in complex with 1H-benzimidazol-2-amine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherinhouse model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527716 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
Crystal Properties
Matthews coefficientSolvent content
3.7867.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.479α = 90
b = 95.479β = 90
c = 116.331γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54178

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
12.15096.90.098.82.731114
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)
12.12.1892.70.6192.32927

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 REPLACEMENTTHROUGHOUTinhouse model2.142.7226774138387.740.1840.18210.2195RANDOM37.758
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]
-0.44-0.440.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.153
r_dihedral_angle_4_deg18.288
r_dihedral_angle_3_deg14.882
r_dihedral_angle_1_deg6.314
r_scangle_it2.774
r_scbond_it1.81
r_mcangle_it1.474
r_angle_refined_deg1.383
r_mcbond_it0.951
r_angle_other_deg0.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.153
r_dihedral_angle_4_deg18.288
r_dihedral_angle_3_deg14.882
r_dihedral_angle_1_deg6.314
r_scangle_it2.774
r_scbond_it1.81
r_mcangle_it1.474
r_angle_refined_deg1.383
r_mcbond_it0.951
r_angle_other_deg0.922
r_symmetry_vdw_other0.228
r_nbd_other0.203
r_nbd_refined0.196
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.164
r_mcbond_other0.16
r_symmetry_hbond_refined0.126
r_metal_ion_refined0.107
r_chiral_restr0.085
r_nbtor_other0.083
r_symmetry_vdw_refined0.069
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2376
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms65

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing