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Structure of alkaline phosphatase from the Antarctic bacterium TAB5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ED9 PDB ENTRY 1ED9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 HANGING-DROP, 4 DEGREE C, 17 MG/ML PROTEIN, 23% PEG3350, 0.2M NAAC, 10MM 4-NITROPHENYL PHOSPHATE, 0.1M CACODYLATE, PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.043 α = 90 b = 173.184 β = 90 c = 55.34 γ = 90
Symmetry Space Group P 21 21 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 CCD 2004-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.95 30 97.3 0.13 12.3 4.2 48685
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 2.06 84.3 0.26 2.3 3
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 1ED9 1.95 8.74 45527 2433 97.2 0.165 0.162 0.1643 0.225 0.2259 RANDOM 19.01
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_4_deg 15.735 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_1_deg 6.787 r_scangle_it 4.57 r_scbond_it 3.365 r_mcangle_it 2.039 r_angle_refined_deg 1.934 r_mcbond_it 1.322 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_4_deg 15.735 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_1_deg 6.787 r_scangle_it 4.57 r_scbond_it 3.365 r_mcangle_it 2.039 r_angle_refined_deg 1.934 r_mcbond_it 1.322 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.287 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.22 r_chiral_restr 0.161 r_xyhbond_nbd_refined 0.152 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5089 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing