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Crystal structure of an acidic, non-myotoxic phospholipase A2 from the venom of Bothrops jararacussu
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GOD PDB ENTRY 1GOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 pH 4.60
Crystal Properties Matthews coefficient Solvent content 1.78 30.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.99 α = 90 b = 53.99 β = 90 c = 90.46 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE MARRESEARCH MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.79 50 94 0.046 22.1 5.7 9034 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.83 80.1 0.153 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GOD 1.79 30.29 8580 429 94.4 0.164 0.161 0.229 RANDOM 16.17
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] -0.01 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.136 r_scangle_it 2.824 r_mcangle_it 2.659 r_angle_refined_deg 2.048 r_scbond_it 1.858 r_mcbond_it 1.716 r_angle_other_deg 1.017 r_symmetry_vdw_other 0.28 r_nbd_other 0.27 r_symmetry_hbond_refined 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.136 r_scangle_it 2.824 r_mcangle_it 2.659 r_angle_refined_deg 2.048 r_scbond_it 1.858 r_mcbond_it 1.716 r_angle_other_deg 1.017 r_symmetry_vdw_other 0.28 r_nbd_other 0.27 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.235 r_xyhbond_nbd_refined 0.231 r_chiral_restr 0.148 r_nbtor_other 0.106 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 949 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing