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Crystal structure of plasmodial PLP synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NV2 PDB ENTRY 2NV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.471 α = 90 b = 180.471 β = 90 c = 102.042 γ = 120
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 MARMOSAIC 225 mm CCD 2009-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.42 50 99.9 0.08 21.6 6.7 24370 46.5
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 2.42 2.46 98.4 0.46 3.1 4.5
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 2NV2 2.42 50 23093 1242 99.88 0.18507 0.18263 0.1868 0.23236 0.2327 RANDOM 44.379
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] -0.19 -0.09 -0.19 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.853 r_dihedral_angle_3_deg 17.532 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_1_deg 6.699 r_scangle_it 4.338 r_scbond_it 2.632 r_angle_refined_deg 1.678 r_mcangle_it 1.674 r_angle_other_deg 1.164 r_mcbond_it 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.853 r_dihedral_angle_3_deg 17.532 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_1_deg 6.699 r_scangle_it 4.338 r_scbond_it 2.632 r_angle_refined_deg 1.678 r_mcangle_it 1.674 r_angle_other_deg 1.164 r_mcbond_it 0.878 r_mcbond_other 0.139 r_chiral_restr 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 4062 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing