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Initial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10 293 PEG 400, Potassium phosphate monobasic, CAPS, DTT, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.3 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.455 α = 90 b = 177.455 β = 90 c = 232.699 γ = 120
Symmetry Space Group P 63 2 2
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 ADSC QUANTUM 210 2004-06-11 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 210 2004-06-20 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-3 SSRL BL11-3 2 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9794, 0.91840, 0.97950 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.85 50 99.3 0.132 8.4 5.3 50738 50574 -3 69.775
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.85 3 96.3 0.708 1.8 4.3 7016
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.85 44.54 47958 47958 2557 99.05 0.23706 0.23706 0.23607 0.2403 0.25576 0.2606 RANDOM 56.225
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.426 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_4_deg 14.453 r_dihedral_angle_1_deg 4.761 r_scangle_it 2.229 r_mcangle_it 1.694 r_scbond_it 1.406 r_mcbond_it 1.011 r_angle_refined_deg 0.944 r_angle_other_deg 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.426 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_4_deg 14.453 r_dihedral_angle_1_deg 4.761 r_scangle_it 2.229 r_mcangle_it 1.694 r_scbond_it 1.406 r_mcbond_it 1.011 r_angle_refined_deg 0.944 r_angle_other_deg 0.73 r_symmetry_vdw_other 0.221 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.171 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.127 r_mcbond_other 0.113 r_symmetry_hbond_refined 0.09 r_nbtor_other 0.081 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8415 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SHARP phasing