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Structure of Cyclophilin A in complex with 2,3-Diaminopyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 Tris, PEG8000
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.535 α = 90 b = 54.477 β = 90 c = 86.808 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 PIXEL DECTRIS PILATUS 300K 2013-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.25 46.15 97.8 0.065 8.7 3.7 55267
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 89.5 0.594 0.443 1 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4n1m 1.25 46.14 52465 2745 97.57 0.1947 0.19342 0.21955 0.233 RANDOM 17.751
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] -0.57 0.8 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.187 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_4_deg 11.522 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 6.337 r_long_range_B_other 6.12 r_scangle_other 3.838 r_scbond_it 2.624 r_scbond_other 2.624 r_mcangle_other 2.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.187 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_4_deg 11.522 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 6.337 r_long_range_B_other 6.12 r_scangle_other 3.838 r_scbond_it 2.624 r_scbond_other 2.624 r_mcangle_other 2.439 r_mcangle_it 2.43 r_angle_refined_deg 2.294 r_mcbond_it 1.653 r_mcbond_other 1.574 r_angle_other_deg 1.179 r_chiral_restr 0.167 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1266 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing