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Crystal Structure of the first nucleotide binding domain of chaperone ClpB1, putative, (Pv089580) from Plasmodium Vivax
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBK 1JBK.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 1.4 M Sodium Citrate
100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.86 33.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.728 α = 90 b = 52.213 β = 90 c = 91.92 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 100 IMAGE PLATE RIGAKU RAXIS IV 2007-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.7 92.06 93.8 0.09 0.092 19.1 6.3 17611 16520
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) 1.7 1.76 67.4 0.34 0.325 5.08 5.1 1167
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1JBK.pdb 1.7 92.06 16711 15670 841 93.77 0.20295 0.20295 0.20103 0.23927 0.2657 RANDOM 21.753
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] -0.69 1.35 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.962 r_dihedral_angle_4_deg 18.827 r_dihedral_angle_3_deg 14.315 r_dihedral_angle_1_deg 5.208 r_scangle_it 2.514 r_scbond_it 1.572 r_angle_refined_deg 1.074 r_mcangle_it 0.828 r_mcbond_it 0.54 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.962 r_dihedral_angle_4_deg 18.827 r_dihedral_angle_3_deg 14.315 r_dihedral_angle_1_deg 5.208 r_scangle_it 2.514 r_scbond_it 1.572 r_angle_refined_deg 1.074 r_mcangle_it 0.828 r_mcbond_it 0.54 r_nbtor_refined 0.297 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.158 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1409 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing