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Calcium pump crystal structure with bound AMPPCP and Ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZBD PDB ENTRY 2ZBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6.1 283 pH 6.1, MICRODIALYSIS, temperature 283K
Crystal Properties Matthews coefficient Solvent content 3.99 69.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.995 α = 90 b = 75.306 β = 108.97 c = 151.541 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 IMAGE PLATE RIGAKU RAXIS V 2004-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.75 SPring-8 BL41XU
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 2.5 50 99.8 0.043 31.8 3.3 59902 59761 -3
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 2.5 2.56 98.5 0.482 2.7 3 4201
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 (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 2ZBD 2.5 15 56359 56359 3001 100 0.24817 0.24688 0.2393 0.27243 0.263 RANDOM 120.795
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] -4.11 -5.28 11.64 -10.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.504 r_dihedral_angle_4_deg 18.971 r_dihedral_angle_3_deg 16.646 r_dihedral_angle_1_deg 3.348 r_scangle_it 2.556 r_mcangle_it 2.063 r_scbond_it 1.634 r_angle_refined_deg 1.252 r_mcbond_it 1.151 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.504 r_dihedral_angle_4_deg 18.971 r_dihedral_angle_3_deg 16.646 r_dihedral_angle_1_deg 3.348 r_scangle_it 2.556 r_mcangle_it 2.063 r_scbond_it 1.634 r_angle_refined_deg 1.252 r_mcbond_it 1.151 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 7674 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 55
Software Software Software Name Purpose BSS data collection CNS refinement REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing