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Crystal structure of the b' domain of human protein disulfide isomerase-like protein of the testis (PDILT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 295 0.2 M sodium formate, 0.1 M Bicine pH 9.0, 18% PEG3350, 0.1 M cobaltous chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.95 37.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.977 α = 90 b = 119.736 β = 90.9 c = 33.291 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 CCD ADSC QUANTUM 210 2007-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9770 CHESS A1
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 2 50 98.93 0.043 24.7 3.2 30405 30080 1 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 2.03 92.8 0.211 4.2 2.8 2079
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 3bj5 2 50 1 1 30405 30080 1607 98.93 0.19739 0.19518 0.1947 0.23828 0.2363 RANDOM 24.697
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] -0.38 0.04 1.44 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 17.229 r_dihedral_angle_3_deg 15.616 r_dihedral_angle_1_deg 4.277 r_scangle_it 1.625 r_scbond_it 0.98 r_angle_refined_deg 0.97 r_mcangle_it 0.749 r_mcbond_it 0.435 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 17.229 r_dihedral_angle_3_deg 15.616 r_dihedral_angle_1_deg 4.277 r_scangle_it 1.625 r_scbond_it 0.98 r_angle_refined_deg 0.97 r_mcangle_it 0.749 r_mcbond_it 0.435 r_nbtor_refined 0.299 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4030 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 12
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling