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Crystal structure of a n-acetylneuraminic acid phosphatase (nanp) from mus musculus at 1.90 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X42 PDb entry 1x42A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 9 277 1.8M (NH4)H2PO3, 0.1M TRIS, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.259 α = 90 b = 71.259 β = 90 c = 195.632 γ = 120
Symmetry Space Group P 61 2 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 QUANTUM 4 2004-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 1.9 50 99.2 0.059 15.6 8.9 24076
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 1.9 1.93 93.8 0.47 3.34 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDb entry 1x42A 1.9 44.82 23709 1209 98.02 0.21 0.208 0.259 0.3072 RANDOM 39.234
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] 0.53 0.26 0.53 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.797 r_dihedral_angle_4_deg 13.85 r_dihedral_angle_3_deg 13.312 r_scangle_it 7.043 r_dihedral_angle_1_deg 5.536 r_scbond_it 5.042 r_mcangle_it 3.093 r_mcbond_it 1.946 r_angle_refined_deg 1.513 r_angle_other_deg 0.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.797 r_dihedral_angle_4_deg 13.85 r_dihedral_angle_3_deg 13.312 r_scangle_it 7.043 r_dihedral_angle_1_deg 5.536 r_scbond_it 5.042 r_mcangle_it 3.093 r_mcbond_it 1.946 r_angle_refined_deg 1.513 r_angle_other_deg 0.794 r_mcbond_other 0.581 r_symmetry_vdw_other 0.255 r_nbd_refined 0.224 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.176 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.112 r_nbtor_other 0.089 r_chiral_restr 0.085 r_symmetry_vdw_refined 0.061 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1882 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing