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Human common-type acylphosphatase variant, A99
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VH7 PDB ENTRY 2VH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 16MG/ML K99A IN 20MMTRIS, 0.2MNACL, PH7.5 K99A WAS CRYSTALLIZED IN 0.1M BIS-TRIS, 0.1M NAOAC, PH6.0 WITH 25% PEG3350 AS CYROPROTECTANT
Crystal Properties Matthews coefficient Solvent content 1.87 34.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.604 α = 90 b = 57.861 β = 90 c = 59.095 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.52 14.31 99.9 0.04 30.7 2 13607 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) 1 1.52 1.52 100 0.18 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 2VH7 1.52 41.34 12894 671 99.8 0.198 0.196 0.2074 0.228 0.237 RANDOM 13.18
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] 0.22 -0.66 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.003 r_dihedral_angle_3_deg 10.902 r_dihedral_angle_4_deg 9.212 r_dihedral_angle_1_deg 7.015 r_scangle_it 3.43 r_scbond_it 2.343 r_mcangle_it 1.529 r_angle_refined_deg 1.353 r_mcbond_it 1.245 r_angle_other_deg 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.003 r_dihedral_angle_3_deg 10.902 r_dihedral_angle_4_deg 9.212 r_dihedral_angle_1_deg 7.015 r_scangle_it 3.43 r_scbond_it 2.343 r_mcangle_it 1.529 r_angle_refined_deg 1.353 r_mcbond_it 1.245 r_angle_other_deg 0.74 r_symmetry_vdw_other 0.235 r_nbd_refined 0.2 r_nbd_other 0.18 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.141 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.09 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 765 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing