5PB5

human factor VIIa in complex with 1-[[3-[5-hydroxy-4-(7H-pyrrolo[2,3-d]pyrimidin-6-yl)pyrazol-1-yl]phenyl]methyl]-3-phenylurea at 1.84A


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
3.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.037α = 90
b = 95.037β = 90
c = 116.512γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54177

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
11.8449.6798.50.0630.06322.229.5746187
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)
11.841.9490.10.3630.3634.57.07

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 model1.8447.51435442320980.1860.18530.1998RANDOM23.166
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]
-0.38-0.380.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.585
r_dihedral_angle_4_deg16.859
r_dihedral_angle_3_deg13.883
r_dihedral_angle_1_deg6.466
r_scangle_it2.85
r_angle_other_deg2.055
r_scbond_it1.662
r_angle_refined_deg1.427
r_mcangle_it1.303
r_mcbond_it0.693
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.585
r_dihedral_angle_4_deg16.859
r_dihedral_angle_3_deg13.883
r_dihedral_angle_1_deg6.466
r_scangle_it2.85
r_angle_other_deg2.055
r_scbond_it1.662
r_angle_refined_deg1.427
r_mcangle_it1.303
r_mcbond_it0.693
r_mcbond_other0.119
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2346
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SADABSdata scaling
PHASERphasing