☰ Navigation Tabs
Crystal structure of protein PTO0218 from Picrophilus torridus, Pfam DUF372
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2 M Calcium Chloride dihydrate, 0.1 M HEPES - Na pH 7.5, 28% v/v Polyethylene Glycol 400, pH 6.5, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.764 α = 90 b = 143.485 β = 90 c = 129.799 γ = 90
Symmetry Space Group C 2 2 21
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 4 2006-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 1.743 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.08 50 96.7 0.056 0.051 59.4 20.2 49920 49920 28.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.15 78.4 0.223 0.224 9 4 3969
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.08 40.2 49920 49892 2532 97.28 0.179 0.179 0.176 0.1762 0.225 0.2262 RANDOM 25.09
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] -0.05 0.54 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.897 r_dihedral_angle_4_deg 16.42 r_dihedral_angle_3_deg 12.173 r_dihedral_angle_1_deg 5.625 r_scangle_it 2.441 r_scbond_it 1.595 r_mcangle_it 1.155 r_angle_refined_deg 1.084 r_mcbond_it 0.704 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.897 r_dihedral_angle_4_deg 16.42 r_dihedral_angle_3_deg 12.173 r_dihedral_angle_1_deg 5.625 r_scangle_it 2.441 r_scbond_it 1.595 r_mcangle_it 1.155 r_angle_refined_deg 1.084 r_mcbond_it 0.704 r_nbtor_refined 0.304 r_nbd_refined 0.194 r_symmetry_metal_ion_refined 0.191 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.125 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5608 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 37
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction SHELXD phasing SHELXE model building CCP4 phasing ARP/wARP model building