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Crystal structure of Cryptosporidium parvum cyclophilin type peptidyl-prolyl cis-trans isomerase cgd2_1660 in the presence of dipeptide ala-pro
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2POE PDB entry 2POE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Tris-HCl pH 8.5, 30 mM ala-pro, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.53 65.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.047 α = 90 b = 69.047 β = 90 c = 124.622 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE RIGAKU RAXIS IV 2007-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 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 2.17 50 99.9 0.066 0.046 53.7 13.8 16658 16658
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 2.17 2.25 100 0.516 0.418 6.2 13.7 1608
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2POE 2.17 24.78 15797 15791 842 99.96 0.227 0.22707 0.22574 0.2178 0.2518 0.2431 RANDOM 39.425
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 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.12 r_dihedral_angle_3_deg 12.997 r_dihedral_angle_1_deg 5.637 r_dihedral_angle_4_deg 2.744 r_scangle_it 1.836 r_scbond_it 1.211 r_angle_refined_deg 1.077 r_mcangle_it 1.022 r_mcbond_it 0.572 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.12 r_dihedral_angle_3_deg 12.997 r_dihedral_angle_1_deg 5.637 r_dihedral_angle_4_deg 2.744 r_scangle_it 1.836 r_scbond_it 1.211 r_angle_refined_deg 1.077 r_mcangle_it 1.022 r_mcbond_it 0.572 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.254 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.06 r_bond_refined_d 0.008 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 1241 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing