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Crystal structure of cyclophilin B at 1.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CYN PDB entry 1CYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 25% w/v PEG 1500, 0.1M MMT buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.665 α = 90 b = 64.665 β = 90 c = 39.463 γ = 120
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 mirrors 2009-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.9795 CHESS F2
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 1.2 50 100 0.035 49.8 5.3 54635 1
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) 1.2 1.22 99.7 0.105 8.8 3.1 3989
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 1CYN 1.2 50 54608 54608 2916 99.92 0.14407 0.14407 0.14312 0.1422 0.16185 0.1609 RANDOM 10.764
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] -0.14 -0.07 -0.14 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.763 r_dihedral_angle_4_deg 20.182 r_dihedral_angle_3_deg 9.366 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.163 r_sphericity_free 1.885 r_scbond_it 1.585 r_sphericity_bonded 1.522 r_rigid_bond_restr 1.239 r_angle_refined_deg 1.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.763 r_dihedral_angle_4_deg 20.182 r_dihedral_angle_3_deg 9.366 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.163 r_sphericity_free 1.885 r_scbond_it 1.585 r_sphericity_bonded 1.522 r_rigid_bond_restr 1.239 r_angle_refined_deg 1.118 r_mcangle_it 0.977 r_mcbond_it 0.623 r_nbtor_refined 0.313 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.146 r_chiral_restr 0.076 r_xyhbond_nbd_refined 0.076 r_symmetry_hbond_refined 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1399 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling