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Combining crystallography and molecular dynamics: The case of Schistosoma mansoni phospholipid glutathione peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1M PDB ENTRY 2V1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.2M NAH2PO4, 0.1M MES, 32% PEG-MME 5000, PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.4 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.913 α = 90 b = 51.17 β = 90 c = 90.622 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 199 CCD MARRESEARCH 2009-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.7 45.31 99.7 0.08 17.3 5.3 21068 2 12.7
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 1.7 1.79 100 0.16 9.3 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V1M 1.7 90.54 19983 1085 99.54 0.18355 0.18203 0.1825 0.21112 0.2104 RANDOM 10.591
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] 0.26 -0.38 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.551 r_dihedral_angle_4_deg 13.178 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 5.847 r_scangle_it 3.266 r_scbond_it 2.254 r_angle_refined_deg 1.406 r_mcangle_it 1.368 r_mcbond_it 0.95 r_symmetry_vdw_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.551 r_dihedral_angle_4_deg 13.178 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 5.847 r_scangle_it 3.266 r_scbond_it 2.254 r_angle_refined_deg 1.406 r_mcangle_it 1.368 r_mcbond_it 0.95 r_symmetry_vdw_refined 0.32 r_nbtor_refined 0.309 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_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 1317 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing