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Crystal structuore of acylphosphatase from Pyrococcus horikoshii complexed with formate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ACY PDB ENTRY 2ACY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 290 0.1M MES PH6 1.4M SODIUM FORMATE 17C, pH 6.00
Crystal Properties Matthews coefficient Solvent content 3.9 68.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.336 α = 90 b = 85.336 β = 90 c = 75.65 γ = 120
Symmetry Space Group P 32 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 CCD ADSC CCD 2003-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 1.5 16.95 99.9 0.08 22.5 9.7 51268 2 15.88
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 1.5 1.58 99.9 0.39 5.2 9.2
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 2ACY 1.5 73.92 48655 2601 99.9 0.167 0.166 0.1753 0.174 0.1842 RANDOM 13.8
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] 0.41 0.2 0.41 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 13.261 r_dihedral_angle_3_deg 11.483 r_dihedral_angle_1_deg 5.764 r_scangle_it 2.964 r_scbond_it 2.15 r_angle_refined_deg 1.199 r_mcangle_it 1.135 r_mcbond_it 1.124 r_angle_other_deg 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 13.261 r_dihedral_angle_3_deg 11.483 r_dihedral_angle_1_deg 5.764 r_scangle_it 2.964 r_scbond_it 2.15 r_angle_refined_deg 1.199 r_mcangle_it 1.135 r_mcbond_it 1.124 r_angle_other_deg 0.77 r_symmetry_vdw_other 0.252 r_nbd_refined 0.194 r_nbd_other 0.19 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.113 r_symmetry_vdw_refined 0.09 r_chiral_restr 0.078 r_nbtor_other 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1434 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing