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Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZD PDB entry 3HZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 20% 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 coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.67 α = 90 b = 62.46 β = 90 c = 87.077 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2006-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.425 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.28 50.77 94.8 12419 11778 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.36 94.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3HZD 2.28 50.77 11778 11778 612 94.31 0.23605 0.23515 0.2554 0.25445 0.2731 RANDOM 48.739
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.257 r_dihedral_angle_4_deg 20.375 r_dihedral_angle_3_deg 20.086 r_angle_refined_deg 3.178 r_scangle_it 2.99 r_mcangle_it 2.435 r_scbond_it 1.966 r_dihedral_angle_1_deg 1.87 r_mcbond_it 1.41 r_nbtor_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.257 r_dihedral_angle_4_deg 20.375 r_dihedral_angle_3_deg 20.086 r_angle_refined_deg 3.178 r_scangle_it 2.99 r_mcangle_it 2.435 r_scbond_it 1.966 r_dihedral_angle_1_deg 1.87 r_mcbond_it 1.41 r_nbtor_refined 0.338 r_nbd_refined 0.335 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.201 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.122 r_gen_planes_refined 0.042 r_bond_refined_d 0.038 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 Atoms Number Protein Atoms 1873 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling