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CYCLOPHILIN 3 complexed with DIPEPTIDE GLY-PRO
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 VAPOR DIFFUSION, HANGING DROP 5.6 291 30% MPEG 5000, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 3.25 61.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.724 α = 90 b = 62.724 β = 90 c = 122.756 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 1.78 36.04 98 0.123 11.7 4.3 23790 25.8
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) 1.78 1.88 90.9 0.01424 0.9 4.2 3131
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 FREE R PDB ENTRY 1E8K 1.78 35.95 23642 22427 1215 92.6 0.2245 0.2245 0.2245 0.2047 0.2637 0.2461 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 7 1436.93
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.075 s_anti_bump_dis_restr 0.05 s_non_zero_chiral_vol 0.037 s_zero_chiral_vol 0.032 s_from_restr_planes 0.0266 s_angle_d 0.023 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 1303 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 12
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling SHELX phasing