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Crystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 28% PEG 2000 MME, 0.1 M Bis-Tris pH 6.5, 1 mM GDP, 2 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K 2 VAPOR DIFFUSION, HANGING DROP 5.2 298 28% PEG 3350, 0.2 M NaCl, 0.1 M Na Cacodylate pH 5.2, 1 mM GDP, 2 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.377 α = 90 b = 77.162 β = 90 c = 40.196 γ = 90
Symmetry Space Group P 21 21 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 315 2007-06-10 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2007-05-03 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID 2 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.01 50 100 0.076 0.041 11.9 6.9 12175 12175
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.01 2.08 100 0.441 0.301 3.25 6.5 1181
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.01 32.72 12151 12139 580 99.99 0.225 0.225 0.223 0.264 0.2676 RANDOM 37.034
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 -0.58 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.189 r_dihedral_angle_4_deg 27.388 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 5.64 r_scangle_it 1.803 r_angle_refined_deg 1.187 r_scbond_it 1.122 r_mcangle_it 1.025 r_mcbond_it 0.578 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.189 r_dihedral_angle_4_deg 27.388 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 5.64 r_scangle_it 1.803 r_angle_refined_deg 1.187 r_scbond_it 1.122 r_mcangle_it 1.025 r_mcbond_it 0.578 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection SHELXD phasing