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Crystal structure of the P- and N-domains of His462Gln mutant CopA, a copper-transporting P-type ATPase, bound with AMPPCP-Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A1C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 5% PEG 6000, 1.5M NaCl, 0.1M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.18 61.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.526 α = 90 b = 90.526 β = 90 c = 191.218 γ = 90
Symmetry Space Group P 43 2 2
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 315 2007-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
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 1.95 20 99.9 0.058 32.3 6.5 55707 49.7
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 1.95 2.01 99.8 0.232 3.1 5.9
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 3A1C 1.95 20 55707 2963 99.96 0.21018 0.20836 0.2056 0.245 0.2409 RANDOM 49.686
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] 0.18 0.18 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.024 r_dihedral_angle_4_deg 19.181 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_1_deg 5.187 r_scangle_it 3.333 r_scbond_it 2.034 r_mcangle_it 1.357 r_angle_refined_deg 1.311 r_mcbond_it 0.813 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.024 r_dihedral_angle_4_deg 19.181 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_1_deg 5.187 r_scangle_it 3.333 r_scbond_it 2.034 r_mcangle_it 1.357 r_angle_refined_deg 1.311 r_mcbond_it 0.813 r_nbtor_refined 0.292 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.181 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_refined 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 4031 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing