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Crystal structure of Plasmodium falciparum Rab11a in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OIV PDB entry 1OIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.9 293 26% PEG 4000, 100mM Na Citrate, 200mM NH4 Acetate, pH 5.9, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.49 α = 90 b = 48.371 β = 92.36 c = 119.236 γ = 90
Symmetry Space Group P 1 21 1
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 Rh-coated Si mirror for vertical focusing 2007-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97700 CHESS A1
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 1.77 50 97.9 0.183 4.8 3.3 91227
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 1.77 1.83 90.5 0.801 2.8 8368
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 1OIV 1.8 19.95 87258 4367 98.36 0.22 0.218 0.2224 0.259 0.2633 RANDOM 20.274
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 -0.07 0.09 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.248 r_dihedral_angle_4_deg 17.331 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 5.563 r_scangle_it 2.6 r_scbond_it 1.707 r_angle_refined_deg 1.342 r_mcangle_it 1.309 r_angle_other_deg 0.977 r_mcbond_it 0.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.248 r_dihedral_angle_4_deg 17.331 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 5.563 r_scangle_it 2.6 r_scbond_it 1.707 r_angle_refined_deg 1.342 r_mcangle_it 1.309 r_angle_other_deg 0.977 r_mcbond_it 0.821 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.206 r_nbd_other 0.194 r_symmetry_vdw_other 0.193 r_nbtor_refined 0.171 r_mcbond_other 0.165 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.081 r_nbtor_other 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6620 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 158
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection