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Plasmodium yoelii cyclophilin-like protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XYH PDB ENTRY 1XYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 296 3.2 M NaCl, 0.1 M Bis-Tris propane, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 4.4 71.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.399 α = 90 b = 132.399 β = 90 c = 132.399 γ = 90
Symmetry Space Group P 41 3 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 IMAGE PLATE RIGAKU RAXIS IV VariMax 2005-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 2.5 46.8 100 0.137 0.137 6.1 38.8 14318 14318 42.1
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) 2.5 2.54 100 0.842 0.842 5.4 39.4 681
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 PDB ENTRY 1XYH 2.5 46.8 13563 13563 718 100 0.19218 0.19218 0.18974 0.24247 0.153 RANDOM 32.127
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 21.622 r_dihedral_angle_3_deg 16.693 r_dihedral_angle_1_deg 7.565 r_scangle_it 4.32 r_scbond_it 2.752 r_angle_refined_deg 2.003 r_mcangle_it 1.735 r_mcbond_it 1.007 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 21.622 r_dihedral_angle_3_deg 16.693 r_dihedral_angle_1_deg 7.565 r_scangle_it 4.32 r_scbond_it 2.752 r_angle_refined_deg 2.003 r_mcangle_it 1.735 r_mcbond_it 1.007 r_nbtor_refined 0.328 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.129 r_symmetry_hbond_refined 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 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 1346 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling PHASER phasing O model building