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Crystal structure of cocaprin 1, inhibitor of cysteine and aspartic proteases from Coprinopsis cinerea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES, 1.3 M Trisodium citrate, pH=7.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.664 α = 90 b = 94.403 β = 103.06 c = 52.151 γ = 90
Symmetry Space Group P 1 21 1
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 6M 2009-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.067170 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.6 34.58 97.2 0.999 26.43 7.397 41795
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 0.869
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2IHO 1.6 34.58 39704 2090 97.3 0.1649 0.163 0.1764 0.2011 0.2105 RANDOM 13.547
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] 0.76 0.15 -0.63 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.17 r_dihedral_angle_4_deg 18.086 r_dihedral_angle_3_deg 12.439 r_dihedral_angle_1_deg 8.256 r_angle_refined_deg 1.677 r_angle_other_deg 1.586 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.17 r_dihedral_angle_4_deg 18.086 r_dihedral_angle_3_deg 12.439 r_dihedral_angle_1_deg 8.256 r_angle_refined_deg 1.677 r_angle_other_deg 1.586 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2096 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing