5PB2

Crystal Structure of Factor VIIa in complex with 2-phenyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-3-ol


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 Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.683α = 90
b = 95.683β = 90
c = 116.746γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.4534.5197.80.0750.07512.866.6894122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.5589.30.5060.5062.034.19

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 model1.4533.8384967446193.020.19620.19580.2036RANDOM17.747
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]
-0.37-0.370.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.779
r_dihedral_angle_4_deg19.176
r_dihedral_angle_3_deg14.074
r_dihedral_angle_1_deg6.202
r_scangle_it2.998
r_angle_other_deg2.671
r_scbond_it1.791
r_angle_refined_deg1.468
r_mcangle_it1.455
r_mcbond_it0.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.779
r_dihedral_angle_4_deg19.176
r_dihedral_angle_3_deg14.074
r_dihedral_angle_1_deg6.202
r_scangle_it2.998
r_angle_other_deg2.671
r_scbond_it1.791
r_angle_refined_deg1.468
r_mcangle_it1.455
r_mcbond_it0.776
r_mcbond_other0.133
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2372
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SADABSdata scaling
PHASERphasing