☰ Navigation Tabs
Crystal structure of APE0912 from Aeropyrum pernix K1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5I PDB ENTRY 1O5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 2.5% PEG 8000, 0.05M Tris-HCl, 0.025M MES-NaOH, 0.1M Sodium chloride, 2.5mM NADPH, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.759 α = 90 b = 68.869 β = 119 c = 69.34 γ = 90
Symmetry Space Group C 1 2 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.6 50 95.1 0.032 33.1 60040
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 1.6 1.66 79.6 0.49 3.1
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 PDB ENTRY 1O5I 1.8 31.19 39359 2128 97.97 0.18882 0.18621 0.1851 0.23732 0.2355 RANDOM 24.218
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] 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.17 r_dihedral_angle_4_deg 15.666 r_dihedral_angle_3_deg 13.784 r_dihedral_angle_1_deg 6.104 r_scangle_it 3.996 r_scbond_it 2.515 r_angle_refined_deg 1.513 r_mcangle_it 1.492 r_mcbond_it 0.892 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.17 r_dihedral_angle_4_deg 15.666 r_dihedral_angle_3_deg 13.784 r_dihedral_angle_1_deg 6.104 r_scangle_it 3.996 r_scbond_it 2.515 r_angle_refined_deg 1.513 r_mcangle_it 1.492 r_mcbond_it 0.892 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.195 r_metal_ion_refined 0.178 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3537 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing