3MWI

The complex crystal Structure of Urokianse and 5-nitro-1H-indole-2-amidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NWNPDB ENTRY 2NWN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62980.05M sodium citrate, 1.95M (NH4)2SO4, 0.05% NaN3, 5% PEG 400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.465α = 90
b = 121.465β = 90
c = 43.097γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002007-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54

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
12.0360.9876.390.03630.076414.954.471174915381
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)
12.0262.04393.010.3590.55215.434.8410290

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 2NWN2.0339.881115359576.520.219180.215130.29655RANDOM13.311
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]
-0.48-0.24-0.480.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.37
r_dihedral_angle_4_deg19.083
r_dihedral_angle_3_deg17.677
r_dihedral_angle_1_deg6.882
r_scangle_it2.834
r_scbond_it1.697
r_angle_refined_deg1.44
r_mcangle_it1.179
r_mcbond_it0.628
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.37
r_dihedral_angle_4_deg19.083
r_dihedral_angle_3_deg17.677
r_dihedral_angle_1_deg6.882
r_scangle_it2.834
r_scbond_it1.697
r_angle_refined_deg1.44
r_mcangle_it1.179
r_mcbond_it0.628
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1941
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms25

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
AMoREphasing
REFMACrefinement
SAINTdata reduction
SCALAdata scaling