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Human common-type acylphosphatase variant, A99G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other HUMAN COMMON-TYPE ACYPHOSPHATASE WILD TYPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 2.4M SODIUM MALONATE, PH7.0 25% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 1.85 33.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.206 α = 90 b = 57.339 β = 90 c = 58.777 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 2006-08-04 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 1.7 41 99.9 0.1 8.5 6.36 9498 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 1.7 1.74 98.4 0.24 2.1
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 HUMAN COMMON-TYPE ACYPHOSPHATASE WILD TYPE 1.7 41.03 9045 453 99.9 0.19 0.187 0.1954 0.241 0.2481 RANDOM 16.24
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] -1.02 -1.14 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.096 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_4_deg 9.829 r_dihedral_angle_1_deg 6.8 r_scangle_it 3.417 r_scbond_it 2.298 r_angle_refined_deg 1.55 r_mcangle_it 1.3 r_mcbond_it 1.097 r_angle_other_deg 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.096 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_4_deg 9.829 r_dihedral_angle_1_deg 6.8 r_scangle_it 3.417 r_scbond_it 2.298 r_angle_refined_deg 1.55 r_mcangle_it 1.3 r_mcbond_it 1.097 r_angle_other_deg 0.848 r_mcbond_other 0.254 r_symmetry_vdw_other 0.227 r_symmetry_hbond_refined 0.22 r_nbd_other 0.197 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.104 r_nbtor_other 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_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 768 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing