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Cyclophilin_5 from C. elegans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E8K PDB ENTRY 1E8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PH 6.0, PEG 4000, LITHIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.4 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.115 α = 90 b = 94.115 β = 90 c = 41.239 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 1.75 24 99.9 0.086 27.7 9.5 21525 3
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 1.75 1.78 100 0.53 3.7 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FREE R-VALUE PDB ENTRY 1E8K 1.75 10 21525 1087 94.8 0.18 0.182 0.1704 0.25 0.228 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2 1608.3
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.069 s_non_zero_chiral_vol 0.049 s_zero_chiral_vol 0.035 s_from_restr_planes 0.0271 s_angle_d 0.023 s_anti_bump_dis_restr 0.016 s_bond_d 0.007 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1402 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 8
Software Software Software Name Purpose SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing