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crystal structure of the P- and N-domains of 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 2B8E PDB ENTRY 2B8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 283 5% PEG 6000, 1.5M NaCl, 0.1M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 3.21 61.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.787 α = 90 b = 90.787 β = 90 c = 191.788 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 2007-09-24 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 99.6 0.081 33.7 6.2 65461 44.9
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 99.1 0.291 2.8 6.2
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 65461 3500 99.76 0.19675 0.19526 0.1938 0.22501 0.2229 RANDOM 44.895
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] 0.17 0.17 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.223 r_dihedral_angle_4_deg 19.17 r_dihedral_angle_3_deg 13.589 r_dihedral_angle_1_deg 5.305 r_scangle_it 3.739 r_scbond_it 2.256 r_mcangle_it 1.388 r_angle_refined_deg 1.341 r_mcbond_it 0.849 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.223 r_dihedral_angle_4_deg 19.17 r_dihedral_angle_3_deg 13.589 r_dihedral_angle_1_deg 5.305 r_scangle_it 3.739 r_scbond_it 2.256 r_mcangle_it 1.388 r_angle_refined_deg 1.341 r_mcbond_it 0.849 r_nbtor_refined 0.297 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.195 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.087 r_metal_ion_refined 0.02 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 4037 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing