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The structure of gene product APE0525 from Aeropyrum pernix
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 K/Na Phosphate, glycerol, ethylene glycol, sucrose, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.85 α = 90 b = 112.792 β = 90 c = 39.001 γ = 90
Symmetry Space Group P 21 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 105 CCD CUSTOM-MADE 2004-12-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97940, 0.97959 APS 19-BM
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 1.85 36.9 94.4 0.079 17.2 4.5 19171 19171
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 79.9 0.434 2.1 2.4
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 MAD THROUGHOUT 1.85 36.86 18045 17112 933 94.44 0.1683 0.1683 0.16668 0.1654 0.19883 0.1979 RANDOM 19.906
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] 0.45 -0.15 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.94 r_dihedral_angle_4_deg 15.492 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.553 r_scangle_it 3.865 r_scbond_it 2.35 r_angle_refined_deg 1.287 r_mcangle_it 1.24 r_mcbond_it 0.644 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.94 r_dihedral_angle_4_deg 15.492 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.553 r_scangle_it 3.865 r_scbond_it 2.35 r_angle_refined_deg 1.287 r_mcangle_it 1.24 r_mcbond_it 0.644 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.209 r_metal_ion_refined 0.181 r_symmetry_metal_ion_refined 0.181 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1470 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing O model building Coot model building CCP4 phasing ARP/wARP model building