3I03

Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HZWPDB entry 3HZW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.828320% w/v PEG 4000, 20% v/v Isopropanol, 0.1 M Sodium citrate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.6653.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.846α = 90
b = 78.294β = 90
c = 66.615γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.425LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.485099.272236122198124.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.53

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3HZW1.4845.982236122198113888.270.207320.206460.22294RANDOM27.884
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]
-0.150.070.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.26
r_dihedral_angle_4_deg22.54
r_dihedral_angle_3_deg14.674
r_dihedral_angle_1_deg4.632
r_scangle_it2.665
r_angle_refined_deg2.177
r_scbond_it1.728
r_mcangle_it1.253
r_mcbond_it0.817
r_nbd_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.26
r_dihedral_angle_4_deg22.54
r_dihedral_angle_3_deg14.674
r_dihedral_angle_1_deg4.632
r_scangle_it2.665
r_angle_refined_deg2.177
r_scbond_it1.728
r_mcangle_it1.253
r_mcbond_it0.817
r_nbd_refined0.341
r_nbtor_refined0.324
r_symmetry_hbond_refined0.174
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_refined0.145
r_chiral_restr0.097
r_gen_planes_refined0.02
r_bond_refined_d0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms952
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms14

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling