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Crystal structure of Calcium ATPase with bound ADP and cyclopiazonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AGV pdb entry 2AGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 284 2.75-3% PEG3350, 25% glycerol, 20 mM MgCl2, 0.1mM EGTA, 20 mM MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 4.26 71.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.498 α = 90 b = 96.836 β = 94.83 c = 154.856 γ = 90
Symmetry Space Group P 1 21 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 210 2005-05-26 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 2005-06-16 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315 2005-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1 2 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11698 ALS 8.3.1 3 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
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 1,2,3 3.4 30 100 0.119 9.5 12.4 25427 2
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) 3.4 3.52 99.8 0.704 7.1 2508
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2AGV 3.4 30 25372 1265 99.49 0.292 0.29 0.328 0.2761 RANDOM 122.587
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] -0.27 0.43 2.55 -2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.703 r_dihedral_angle_3_deg 19.446 r_dihedral_angle_4_deg 17.94 r_dihedral_angle_1_deg 4.677 r_angle_refined_deg 1.274 r_symmetry_vdw_refined 0.351 r_nbtor_refined 0.332 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.703 r_dihedral_angle_3_deg 19.446 r_dihedral_angle_4_deg 17.94 r_dihedral_angle_1_deg 4.677 r_angle_refined_deg 1.274 r_symmetry_vdw_refined 0.351 r_nbtor_refined 0.332 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7562 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction