3HZW

Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HZDPDB entry 3HZD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629120% w/v PEG 4000, 20% w/v Isopropanol, 0.1 M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4750.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.67α = 90
b = 62.46β = 90
c = 87.077γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.425LNLSD03B-MX1

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
12.2850.7794.812419117781
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.3694.8

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 3HZD2.2850.77117781177861294.310.236050.235150.25445RANDOM48.739
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]
2.03-0.61-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.257
r_dihedral_angle_4_deg20.375
r_dihedral_angle_3_deg20.086
r_angle_refined_deg3.178
r_scangle_it2.99
r_mcangle_it2.435
r_scbond_it1.966
r_dihedral_angle_1_deg1.87
r_mcbond_it1.41
r_nbtor_refined0.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.257
r_dihedral_angle_4_deg20.375
r_dihedral_angle_3_deg20.086
r_angle_refined_deg3.178
r_scangle_it2.99
r_mcangle_it2.435
r_scbond_it1.966
r_dihedral_angle_1_deg1.87
r_mcbond_it1.41
r_nbtor_refined0.338
r_nbd_refined0.335
r_symmetry_vdw_refined0.225
r_xyhbond_nbd_refined0.201
r_symmetry_hbond_refined0.141
r_chiral_restr0.122
r_gen_planes_refined0.042
r_bond_refined_d0.038
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 Atoms1873
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms24

Software

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