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Crystal structure of the P- and N-domains of CopA, a copper-transporting P-type ATPase, bound with ADP-Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B8E PDB ENTRY 2B8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 283 pH 5.5, temperature 283K
Crystal Properties Matthews coefficient Solvent content 3.13 60.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.956 α = 90 b = 89.956 β = 90 c = 190.375 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 2007-07-11 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 1.85 20 99.9 0.129 30.6 3.6 63866 41
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 1.85 1.9 100 0.483 5.8 3.4
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 2B8E 1.85 20 63866 3413 99.79 0.19379 0.19213 0.1915 0.22563 0.2237 RANDOM 41.004
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] 0.09 0.09 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_4_deg 17.486 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_1_deg 5.227 r_scangle_it 3.61 r_scbond_it 2.174 r_mcangle_it 1.312 r_angle_refined_deg 1.285 r_mcbond_it 0.81 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_4_deg 17.486 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_1_deg 5.227 r_scangle_it 3.61 r_scbond_it 2.174 r_mcangle_it 1.312 r_angle_refined_deg 1.285 r_mcbond_it 0.81 r_nbtor_refined 0.295 r_metal_ion_refined 0.257 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.079 r_bond_refined_d 0.011 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_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 4033 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing