5PAA

Crystal Structure of Factor VIIa in complex with cyclohexylmethanamine


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
3.7667.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.298α = 90
b = 95.298β = 90
c = 116.041γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5419

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
11.985098.10.1287.36.937204
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)
11.982.0581.50.9123.73013

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 model1.9847.6730785162285.920.1860.18460.2145RANDOM30.461
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]
-0.53-0.531.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.058
r_dihedral_angle_4_deg17.605
r_dihedral_angle_3_deg14.807
r_dihedral_angle_1_deg6.244
r_scangle_it2.689
r_scbond_it1.748
r_mcangle_it1.453
r_angle_refined_deg1.296
r_mcbond_it0.936
r_angle_other_deg0.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.058
r_dihedral_angle_4_deg17.605
r_dihedral_angle_3_deg14.807
r_dihedral_angle_1_deg6.244
r_scangle_it2.689
r_scbond_it1.748
r_mcangle_it1.453
r_angle_refined_deg1.296
r_mcbond_it0.936
r_angle_other_deg0.872
r_symmetry_vdw_other0.204
r_nbd_other0.202
r_nbd_refined0.188
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.169
r_mcbond_other0.157
r_symmetry_hbond_refined0.143
r_nbtor_other0.082
r_chiral_restr0.076
r_metal_ion_refined0.062
r_symmetry_vdw_refined0.052
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2376
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms40

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing