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Crystal Structure of Pyrococcus horikoshii CutA1 Complexed with Cu2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J2V PDB ENTRY 1j2v
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 293 100mM acetate buffer, 1.5M ammonium sulfate, 2mM CuSO4, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.73 28.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.242 α = 90 b = 52.242 β = 90 c = 54.111 γ = 120
Symmetry Space Group P 3 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 4 2003-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.45 40 99.8 0.052 9.3 7.1 15562 15562 -3 11.781
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 1.45 1.5 99.7 0.36 7.2 1532
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1j2v 1.45 10 13822 13822 1555 99.33 0.165 0.16488 0.16168 0.1627 0.19415 0.1919 RANDOM 10.696
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.396 r_scangle_it 3.981 r_scbond_it 2.531 r_mcangle_it 1.649 r_angle_refined_deg 1.478 r_mcbond_it 0.874 r_angle_other_deg 0.797 r_symmetry_hbond_refined 0.376 r_symmetry_vdw_other 0.354 r_nbd_other 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.396 r_scangle_it 3.981 r_scbond_it 2.531 r_mcangle_it 1.649 r_angle_refined_deg 1.478 r_mcbond_it 0.874 r_angle_other_deg 0.797 r_symmetry_hbond_refined 0.376 r_symmetry_vdw_other 0.354 r_nbd_other 0.26 r_xyhbond_nbd_refined 0.241 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.145 r_chiral_restr 0.087 r_nbtor_other 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 873 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement